changeset 24:48d71bd383a1 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/differential_count_models/.hg_archival.txt	Wed Aug 07 01:58:28 2013 -0400
@@ -0,0 +1,5 @@
+repo: 2122e630b13aedc43ced5f83c11988903db28ea6
+node: 37b851eb82033c12fdb550e847e8b40ee302b3c8
+branch: default
+latesttag: null
+latesttagdistance: 24

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/differential_count_models/rgToolFactory.py	Wed Aug 07 01:58:28 2013 -0400
@@ -0,0 +1,631 @@
+# rgToolFactory.py
+# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
+# 
+# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
+# 
+# all rights reserved
+# Licensed under the LGPL
+# suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
+#
+# august 2013
+# found a problem with GS if $TMP or $TEMP missing - now inject /tmp and warn
+#
+# july 2013
+# added ability to combine images and individual log files into html output
+# just make sure there's a log file foo.log and it will be output
+# together with all images named like "foo_*.pdf
+# otherwise old format for html
+#
+# January 2013
+# problem pointed out by Carlos Borroto
+# added escaping for <>$ - thought I did that ages ago...
+#
+# August 11 2012 
+# changed to use shell=False and cl as a sequence
+
+# This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
+# It also serves as the wrapper for the new tool.
+# 
+# you paste and run your script
+# Only works for simple scripts that read one input from the history.
+# Optionally can write one new history dataset,
+# and optionally collect any number of outputs into links on an autogenerated HTML page.
+
+# DO NOT install on a public or important site - please.
+
+# installed generated tools are fine if the script is safe.
+# They just run normally and their user cannot do anything unusually insecure
+# but please, practice safe toolshed.
+# Read the fucking code before you install any tool 
+# especially this one
+
+# After you get the script working on some test data, you can
+# optionally generate a toolshed compatible gzip file
+# containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
+# safe and largely automated installation in a production Galaxy.
+
+# If you opt for an HTML output, you get all the script outputs arranged
+# as a single Html history item - all output files are linked, thumbnails for all the pdfs.
+# Ugly but really inexpensive.
+# 
+# Patches appreciated please. 
+#
+#
+# long route to June 2012 product
+# Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them
+# derived from an integrated script model  
+# called rgBaseScriptWrapper.py
+# Note to the unwary:
+#   This tool allows arbitrary scripting on your Galaxy as the Galaxy user
+#   There is nothing stopping a malicious user doing whatever they choose
+#   Extremely dangerous!!
+#   Totally insecure. So, trusted users only
+#
+# preferred model is a developer using their throw away workstation instance - ie a private site.
+# no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.
+#
+
+import sys 
+import shutil 
+import subprocess 
+import os 
+import time 
+import tempfile 
+import optparse
+import tarfile
+import re
+import shutil
+import math
+
+progname = os.path.split(sys.argv[0])[1] 
+myversion = 'V000.2 June 2012' 
+verbose = False 
+debug = False
+toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
+
+def timenow():
+    """return current time as a string
+    """
+    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
+
+html_escape_table = {
+     "&": "&amp;",
+     ">": "&gt;",
+     "<": "&lt;",
+     "$": "\$"
+     }
+
+def html_escape(text):
+     """Produce entities within text."""
+     return "".join(html_escape_table.get(c,c) for c in text)
+
+def cmd_exists(cmd):
+     return subprocess.call("type " + cmd, shell=True, 
+           stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
+
+
+class ScriptRunner:
+    """class is a wrapper for an arbitrary script
+    """
+
+    def __init__(self,opts=None,treatbashSpecial=True):
+        """
+        cleanup inputs, setup some outputs
+        
+        """
+        self.useGM = cmd_exists('gm')
+        self.useIM = cmd_exists('convert')
+        self.useGS = cmd_exists('gs')
+        self.temp_warned = False # we want only one warning if $TMP not set
+        self.treatbashSpecial = treatbashSpecial
+        if opts.output_dir: # simplify for the tool tarball
+            os.chdir(opts.output_dir)
+        self.thumbformat = 'png'
+        self.opts = opts
+        self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
+        self.toolid = self.toolname
+        self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
+        self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
+        self.xmlfile = '%s.xml' % self.toolname
+        s = open(self.opts.script_path,'r').readlines()
+        s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
+        self.script = '\n'.join(s)
+        fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
+        tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
+        tscript.write(self.script)
+        tscript.close()
+        self.indentedScript = '\n'.join([' %s' % x for x in s]) # for restructured text in help
+        self.escapedScript = '\n'.join([html_escape(x) for x in s])
+        self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
+        if opts.output_dir: # may not want these complexities 
+            self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
+            art = '%s.%s' % (self.toolname,opts.interpreter)
+            artpath = os.path.join(self.opts.output_dir,art) # need full path
+            artifact = open(artpath,'w') # use self.sfile as script source for Popen
+            artifact.write(self.script)
+            artifact.close()
+        self.cl = []
+        self.html = []
+        a = self.cl.append
+        a(opts.interpreter)
+        if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
+            a(self.sfile)
+        else:
+            a('-') # stdin
+        a(opts.input_tab)
+        a(opts.output_tab)
+        self.outFormats = 'tabular' # TODO make this an option at tool generation time
+        self.inputFormats = 'tabular' # TODO make this an option at tool generation time
+        self.test1Input = '%s_test1_input.xls' % self.toolname
+        self.test1Output = '%s_test1_output.xls' % self.toolname
+        self.test1HTML = '%s_test1_output.html' % self.toolname
+
+    def makeXML(self):
+        """
+        Create a Galaxy xml tool wrapper for the new script as a string to write out
+        fixme - use templating or something less fugly than this example of what we produce
+
+        <tool id="reverse" name="reverse" version="0.01">
+            <description>a tabular file</description>
+            <command interpreter="python">
+            reverse.py --script_path "$runMe" --interpreter "python" 
+            --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file" 
+            </command>
+            <inputs>
+            <param name="input1"  type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
+
+            </inputs>
+            <outputs>
+            <data format="tabular" name="tab_file" label="${job_name}"/>
+
+            </outputs>
+            <help>
+            
+**What it Does**
+
+Reverse the columns in a tabular file
+
+            </help>
+            <configfiles>
+            <configfile name="runMe">
+            
+# reverse order of columns in a tabular file
+import sys
+inp = sys.argv[1]
+outp = sys.argv[2]
+i = open(inp,'r')
+o = open(outp,'w')
+for row in i:
+     rs = row.rstrip().split('\t')
+     rs.reverse()
+     o.write('\t'.join(rs))
+     o.write('\n')
+i.close()
+o.close()
+ 
+
+            </configfile>
+            </configfiles>
+            </tool>
+        
+        """ 
+        newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
+            %(tooldesc)s
+            %(command)s
+            <inputs>
+            %(inputs)s
+            </inputs>
+            <outputs>
+            %(outputs)s
+            </outputs>
+            <configfiles>
+            <configfile name="runMe">
+            %(script)s
+            </configfile>
+            </configfiles>
+            %(tooltests)s
+            <help>
+            %(help)s
+            </help>
+            </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
+               
+        newCommand="""<command interpreter="python">
+            %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" 
+            --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s 
+            </command>""" # may NOT be an input or htmlout
+        tooltestsTabOnly = """<tests><test>
+        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
+        <param name="job_name" value="test1"/>
+        <param name="runMe" value="$runMe"/>
+        <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
+        </test></tests>"""
+        tooltestsHTMLOnly = """<tests><test>
+        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
+        <param name="job_name" value="test1"/>
+        <param name="runMe" value="$runMe"/>
+        <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
+        </test></tests>"""
+        tooltestsBoth = """<tests><test>
+        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
+        <param name="job_name" value="test1"/>
+        <param name="runMe" value="$runMe"/>
+        <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
+        <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
+        </test></tests>"""
+        xdict = {}
+        xdict['tool_version'] = self.opts.tool_version
+        xdict['test1Input'] = self.test1Input
+        xdict['test1HTML'] = self.test1HTML
+        xdict['test1Output'] = self.test1Output   
+        if self.opts.make_HTML and self.opts.output_tab <> 'None':
+            xdict['tooltests'] = tooltestsBoth % xdict
+        elif self.opts.make_HTML:
+            xdict['tooltests'] = tooltestsHTMLOnly % xdict
+        else:
+            xdict['tooltests'] = tooltestsTabOnly % xdict
+        xdict['script'] = self.escapedScript 
+        # configfile is least painful way to embed script to avoid external dependencies
+        # but requires escaping of <, > and $ to avoid Mako parsing
+        if self.opts.help_text:
+            xdict['help'] = open(self.opts.help_text,'r').read()
+        else:
+            xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'
+        coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']
+        coda.append(self.indentedScript)
+        coda.append('**Attribution** This Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.' % (self.opts.user_email,timenow()))
+        coda.append('See %s for details of that project' % (toolFactoryURL))
+        coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ')
+        coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573')
+        xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
+        if self.opts.tool_desc:
+            xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
+        else:
+            xdict['tooldesc'] = ''
+        xdict['command_outputs'] = '' 
+        xdict['outputs'] = '' 
+        if self.opts.input_tab <> 'None':
+            xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something
+            xdict['inputs'] = '<param name="input1"  type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats
+        else:
+            xdict['command_inputs'] = '' # assume no input - eg a random data generator       
+            xdict['inputs'] = ''
+        xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
+        xdict['toolname'] = self.toolname
+        xdict['toolid'] = self.toolid
+        xdict['interpreter'] = self.opts.interpreter
+        xdict['scriptname'] = self.sfile
+        if self.opts.make_HTML:
+            xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" '
+            xdict['outputs'] +=  ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
+        if self.opts.output_tab <> 'None':
+            xdict['command_outputs'] += ' --output_tab "$tab_file"'
+            xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
+        xdict['command'] = newCommand % xdict
+        xmls = newXML % xdict
+        xf = open(self.xmlfile,'w')
+        xf.write(xmls)
+        xf.write('\n')
+        xf.close()
+        # ready for the tarball
+
+
+    def makeTooltar(self):
+        """
+        a tool is a gz tarball with eg
+        /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
+        """
+        retval = self.run()
+        if retval:
+            print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
+            sys.exit(1)
+        self.makeXML()
+        tdir = self.toolname
+        os.mkdir(tdir)
+        if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
+            testdir = os.path.join(tdir,'test-data')
+            os.mkdir(testdir) # make tests directory
+            shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
+            if self.opts.output_tab <> 'None':
+                shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
+            if self.opts.make_HTML:
+                shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
+            if self.opts.output_dir:
+                shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
+        op = '%s.py' % self.toolname # new name
+        outpiname = os.path.join(tdir,op) # path for the tool tarball
+        pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
+        notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op,pyin,pyin),]
+        notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
+        notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
+        pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
+        notes += pi
+        outpi = open(outpiname,'w')
+        outpi.write(''.join(notes))
+        outpi.write('\n')
+        outpi.close()
+        stname = os.path.join(tdir,self.sfile)
+        if not os.path.exists(stname):
+            shutil.copyfile(self.sfile, stname)
+        xtname = os.path.join(tdir,self.xmlfile)
+        if not os.path.exists(xtname):
+            shutil.copyfile(self.xmlfile,xtname)
+        tarpath = "%s.gz" % self.toolname
+        tar = tarfile.open(tarpath, "w:gz")
+        tar.add(tdir,arcname=self.toolname)
+        tar.close()
+        shutil.copyfile(tarpath,self.opts.new_tool)
+        shutil.rmtree(tdir)
+        ## TODO: replace with optional direct upload to local toolshed?
+        return retval
+
+
+    def compressPDF(self,inpdf=None,thumbformat='png'):
+        """need absolute path to pdf
+           note that GS gets confoozled if no $TMP or $TEMP
+           so we set it
+        """
+        assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
+        our_env = os.environ.copy()
+        if not (our_env.get('TMP',None) or our_env.get('TEMP',None)):
+            our_env['TMP'] = '/tmp'
+            if not self.temp_warned:
+               print >> sys.stdout,'## WARNING - no $TMP or $TEMP!!! Please fix - using /tmp temporarily'
+               self.temp_warned = True          
+        hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
+        sto = open(hlog,'w')
+        outpdf = '%s_compressed' % inpdf
+        cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
+        x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
+        retval1 = x.wait()
+        sto.close()
+        if retval1 == 0:
+            os.unlink(inpdf)
+            shutil.move(outpdf,inpdf)
+            os.unlink(hlog)
+        else:
+            x = open(hlog,'r').readlines()
+            print >> sys.stdout,x
+        hlog = os.path.join(self.opts.output_dir,"thumbnail_%s.txt" % os.path.basename(inpdf))
+        sto = open(hlog,'w')
+        outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
+        if self.useGM:        
+            cl2 = ['gm', 'convert', inpdf, outpng]
+        else: # assume imagemagick
+            cl2 = ['convert', inpdf, outpng]
+        x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir,env=our_env)
+        retval2 = x.wait()
+        sto.close()
+        if retval2 <> 0:
+             x = open(hlog,'r').readlines()
+             print >> sys.stdout,x
+        else:
+             os.unlink(hlog)
+        retval = retval1 or retval2
+        return retval
+
+
+    def getfSize(self,fpath,outpath):
+        """
+        format a nice file size string
+        """
+        size = ''
+        fp = os.path.join(outpath,fpath)
+        if os.path.isfile(fp):
+            size = '0 B'
+            n = float(os.path.getsize(fp))
+            if n > 2**20:
+                size = '%1.1f MB' % (n/2**20)
+            elif n > 2**10:
+                size = '%1.1f KB' % (n/2**10)
+            elif n > 0:
+                size = '%d B' % (int(n))
+        return size
+
+    def makeHtml(self):
+        """ Create an HTML file content to list all the artifacts found in the output_dir
+        """
+
+        galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> 
+        <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> 
+        <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> 
+        <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> 
+        <title></title> 
+        <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> 
+        </head> 
+        <body> 
+        <div class="toolFormBody"> 
+        """ 
+        galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>""" 
+        galhtmlpostfix = """</div></body></html>\n"""
+
+        flist = os.listdir(self.opts.output_dir)
+        flist = [x for x in flist if x <> 'Rplots.pdf']
+        flist.sort()
+        html = []
+        html.append(galhtmlprefix % progname)
+        html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
+        fhtml = []
+        if len(flist) > 0:
+            logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
+            logfiles.sort()
+            logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)]
+            logfiles.append(os.path.abspath(self.tlog)) # make it the last one
+            pdflist = []
+            npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
+            for rownum,fname in enumerate(flist):
+                dname,e = os.path.splitext(fname)
+                sfsize = self.getfSize(fname,self.opts.output_dir)
+                if e.lower() == '.pdf' : # compress and make a thumbnail
+                    thumb = '%s.%s' % (dname,self.thumbformat)
+                    pdff = os.path.join(self.opts.output_dir,fname)
+                    retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
+                    if retval == 0:
+                        pdflist.append((fname,thumb))
+                    else:
+                        pdflist.append((fname,fname))
+                if (rownum+1) % 2 == 0:
+                    fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
+                else:
+                    fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
+            for logfname in logfiles: # expect at least tlog - if more
+                if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later
+                    sectionname = 'All tool run'
+                    if (len(logfiles) > 1):
+                        sectionname = 'Other'
+                    ourpdfs = pdflist
+                else:
+                    realname = os.path.basename(logfname)
+                    sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
+                    ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
+                    pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
+                nacross = 1
+                npdf = len(ourpdfs)
+
+                if npdf > 0:
+                    nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
+                    if int(nacross)**2 != npdf:
+                        nacross += 1
+                    nacross = int(nacross)
+                    width = min(400,int(1200/nacross))
+                    html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
+                    html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
+                    ntogo = nacross # counter for table row padding with empty cells
+                    html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
+                    for i,paths in enumerate(ourpdfs): 
+                        fname,thumb = paths
+                        s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d" 
+                           alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
+                        if ((i+1) % nacross == 0):
+                            s += '</tr>\n'
+                            ntogo = 0
+                            if i < (npdf - 1): # more to come
+                               s += '<tr>'
+                               ntogo = nacross
+                        else:
+                            ntogo -= 1
+                        html.append(s)
+                    if html[-1].strip().endswith('</tr>'):
+                        html.append('</table></div>\n')
+                    else:
+                        if ntogo > 0: # pad
+                           html.append('<td>&nbsp;</td>'*ntogo)
+                        html.append('</tr></table></div>\n')
+                logt = open(logfname,'r').readlines()
+                logtext = [x for x in logt if x.strip() > '']
+                html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
+                if len(logtext) > 1:
+                    html.append('\n<pre>\n')
+                    html += logtext
+                    html.append('\n</pre>\n')
+                else:
+                    html.append('%s is empty<br/>' % logfname)
+        if len(fhtml) > 0:
+           fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n')
+           fhtml.append('</table></div><br/>')
+           html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
+           html += fhtml # add all non-pdf files to the end of the display
+        else:
+            html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
+        html.append(galhtmlpostfix)
+        htmlf = file(self.opts.output_html,'w')
+        htmlf.write('\n'.join(html))
+        htmlf.write('\n')
+        htmlf.close()
+        self.html = html
+
+
+    def run(self):
+        """
+        scripts must be small enough not to fill the pipe!
+        """
+        if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
+          retval = self.runBash()
+        else:
+            if self.opts.output_dir:
+                ste = open(self.elog,'w')
+                sto = open(self.tlog,'w')
+                sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
+                sto.flush()
+                p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
+            else:
+                p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
+            p.stdin.write(self.script)
+            p.stdin.close()
+            retval = p.wait()
+            if self.opts.output_dir:
+                sto.close()
+                ste.close()
+                err = open(self.elog,'r').readlines()
+                if retval <> 0 and err: # problem
+                    print >> sys.stderr,err
+            if self.opts.make_HTML:
+                self.makeHtml()
+        return retval
+
+    def runBash(self):
+        """
+        cannot use - for bash so use self.sfile
+        """
+        if self.opts.output_dir:
+            s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
+            sto = open(self.tlog,'w')
+            sto.write(s)
+            sto.flush()
+            p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
+        else:
+            p = subprocess.Popen(self.cl,shell=False)            
+        retval = p.wait()
+        if self.opts.output_dir:
+            sto.close()
+        if self.opts.make_HTML:
+            self.makeHtml()
+        return retval
+  
+
+def main():
+    u = """
+    This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
+    <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
+    </command>
+    """
+    op = optparse.OptionParser()
+    a = op.add_option
+    a('--script_path',default=None)
+    a('--tool_name',default=None)
+    a('--interpreter',default=None)
+    a('--output_dir',default=None)
+    a('--output_html',default=None)
+    a('--input_tab',default="None")
+    a('--output_tab',default="None")
+    a('--user_email',default='Unknown')
+    a('--bad_user',default=None)
+    a('--make_Tool',default=None)
+    a('--make_HTML',default=None)
+    a('--help_text',default=None)
+    a('--tool_desc',default=None)
+    a('--new_tool',default=None)
+    a('--tool_version',default=None)
+    opts, args = op.parse_args()
+    assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user)
+    assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
+    assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
+    assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
+    if opts.output_dir:
+        try:
+            os.makedirs(opts.output_dir)
+        except:
+            pass
+    r = ScriptRunner(opts)
+    if opts.make_Tool:
+        retcode = r.makeTooltar()
+    else:
+        retcode = r.run()
+    os.unlink(r.sfile)
+    if retcode:
+        sys.exit(retcode) # indicate failure to job runner
+
+
+if __name__ == "__main__":
+    main()
+
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/differential_count_models/rgedgeRpaired.xml	Wed Aug 07 01:58:28 2013 -0400
@@ -0,0 +1,1084 @@
+<tool id="rgDifferentialCount" name="Differential_Count" version="0.20">
+  <description>models using BioConductor packages</description>
+  <requirements>
+      <requirement type="package" version="2.12">biocbasics</requirement>
+      <requirement type="package" version="3.0.1">r3</requirement>
+      <requirement type="package" version="1.3.18">graphicsmagick</requirement>
+      <requirement type="package" version="9.07">ghostscript</requirement>
+  </requirements>
+  
+  <command interpreter="python">
+     rgToolFactory.py --script_path "$runme" --interpreter "Rscript" --tool_name "DifferentialCounts" 
+    --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
+  </command>
+  <inputs>
+    <param name="input1"  type="data" format="tabular" label="Select an input matrix - rows are contigs, columns are counts for each sample"
+       help="Use the HTSeq based count matrix preparation tool to create these matrices from BAM/SAM files and a GTF file of genomic features"/>
+    <param name="title" type="text" value="Differential Counts" size="80" label="Title for job outputs" 
+           help="Supply a meaningful name here to remind you what the outputs contain">
+      <sanitizer invalid_char="">
+        <valid initial="string.letters,string.digits"><add value="_" /> </valid>
+      </sanitizer>
+    </param>
+    <param name="treatment_name" type="text" value="Treatment" size="50" label="Treatment Name"/>
+    <param name="Treat_cols" label="Select columns containing treatment." type="data_column" data_ref="input1" numerical="True" 
+         multiple="true" use_header_names="true" size="120" display="checkboxes">
+        <validator type="no_options" message="Please select at least one column."/>
+    </param>
+    <param name="control_name" type="text" value="Control" size="50" label="Control Name"/>
+    <param name="Control_cols" label="Select columns containing control." type="data_column" data_ref="input1" numerical="True" 
+         multiple="true" use_header_names="true" size="120" display="checkboxes" optional="true">
+    </param>
+    <param name="subjectids" type="text" optional="true" size="120" value = ""
+       label="IF SUBJECTS NOT ALL INDEPENDENT! Enter comma separated strings to indicate sample labels for (eg) pairing - must be one for every column in input"
+       help="Leave blank if no pairing, but eg if data from sample id A99 is in columns 2,4 and id C21 is in 3,5 then enter 'A99,C21,A99,C21'">
+      <sanitizer>
+        <valid initial="string.letters,string.digits"><add value="," /> </valid>
+      </sanitizer>
+    </param>
+    <param name="fQ" type="float" value="0.3" size="5" label="Non-differential contig count quantile threshold - zero to analyze all non-zero read count contigs"
+     help="May be a good or a bad idea depending on the biology and the question. EG 0.3 = sparsest 30% of contigs with at least one read are removed before analysis"/>
+    <param name="useNDF" type="boolean" truevalue="T" falsevalue="F" checked="false" size="1" 
+              label="Non differential filter - remove contigs below a threshold (1 per million) for half or more samples"
+     help="May be a good or a bad idea depending on the biology and the question. This was the old default. Quantile based is available as an alternative"/>
+
+    <conditional name="edgeR">
+        <param name="doedgeR" type="select" 
+           label="Run this model using edgeR"
+           help="edgeR uses a negative binomial model and seems to be powerful, even with few replicates">
+          <option value="F">Do not run edgeR</option>
+          <option value="T" selected="true">Run edgeR</option>
+         </param>
+         <when value="T">
+          <param name="edgeR_priordf" type="integer" value="20" size="3" 
+           label="prior.df for tagwise dispersion - lower value = more emphasis on each tag's variance. Replaces prior.n  and prior.df = prior.n * residual.df"
+           help="0 = Use edgeR default. Use a small value to 'smooth' small samples. See edgeR docs and note below"/>
+         </when>
+         <when value="F"></when>
+    </conditional>
+    <conditional name="DESeq2">
+    <param name="doDESeq2" type="select" 
+       label="Run the same model with DESeq2 and compare findings"
+       help="DESeq2 is an update to the DESeq package. It uses different assumptions and methods to edgeR">
+      <option value="F" selected="true">Do not run DESeq2</option>
+      <option value="T">Run DESeq2</option>
+     </param>
+     <when value="T">
+         <param name="DESeq_fitType" type="select">
+            <option value="parametric" selected="true">Parametric (default) fit for dispersions</option>
+            <option value="local">Local fit - this will automagically be used if parametric fit fails</option>
+            <option value="mean">Mean dispersion fit- use this if you really understand what you're doing - read the fine manual linked below in the documentation</option>
+         </param> 
+     </when>
+     <when value="F"> </when>
+    </conditional>
+    <param name="doVoom" type="select" 
+       label="Run the same model with Voom/limma and compare findings"
+       help="Voom uses counts per million and a precise transformation of variance so count data can be analysed using limma">
+      <option value="F" selected="true">Do not run VOOM</option>
+      <option value="T">Run VOOM</option>
+     </param>
+    <!--
+    <conditional name="camera">
+        <param name="doCamera" type="select" label="Run the edgeR implementation of Camera GSEA for up/down gene sets" 
+            help="If yes, you can choose a set of genesets to test and/or supply a gmt format geneset collection from your history">
+        <option value="F" selected="true">Do not run GSEA tests with the Camera algorithm</option>
+        <option value="T">Run GSEA tests with the Camera algorithm</option>
+        </param>
+         <when value="T">
+         <conditional name="gmtSource">
+          <param name="refgmtSource" type="select" 
+             label="Use a gene set (.gmt) from your history and/or use a built-in (MSigDB etc) gene set">
+            <option value="indexed" selected="true">Use a built-in gene set</option>
+            <option value="history">Use a gene set from my history</option>
+            <option value="both">Add a gene set from my history to a built in gene set</option>
+          </param>
+          <when value="indexed">
+            <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis">
+              <options from_data_table="gseaGMT_3.1">
+                <filter type="sort_by" column="2" />
+                <validator type="no_options" message="No GMT v3.1 files are available - please install them"/>
+              </options>
+            </param>
+          </when>
+          <when value="history">
+            <param name="ownGMT" type="data" format="gmt" label="Select a Gene Set from your history" />
+          </when>
+          <when value="both">
+            <param name="ownGMT" type="data" format="gseagmt" label="Select a Gene Set from your history" />
+            <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis">
+              <options from_data_table="gseaGMT_4">
+                <filter type="sort_by" column="2" />
+                <validator type="no_options" message="No GMT v4 files are available - please fix tool_data_table and loc files"/>
+              </options>
+            </param>
+           </when>
+         </conditional>
+         </when>
+         <when value="F"> 
+         </when>
+    </conditional>
+    -->
+    <param name="fdrthresh" type="float" value="0.05" size="5" label="P value threshold for FDR filtering for amily wise error rate control"
+     help="Conventional default value of 0.05 recommended"/>
+    <param name="fdrtype" type="select" label="FDR (Type II error) control method" 
+         help="Use fdr or bh typically to control for the number of tests in a reliable way">
+            <option value="fdr" selected="true">fdr</option>
+            <option value="BH">Benjamini Hochberg</option>
+            <option value="BY">Benjamini Yukateli</option>
+            <option value="bonferroni">Bonferroni</option>
+            <option value="hochberg">Hochberg</option>
+            <option value="holm">Holm</option>
+            <option value="hommel">Hommel</option>
+            <option value="none">no control for multiple tests</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out_edgeR" label="${title}_topTable_edgeR.xls">
+         <filter>edgeR['doedgeR'] == "T"</filter>
+    </data>
+    <data format="tabular" name="out_DESeq2" label="${title}_topTable_DESeq2.xls">
+         <filter>DESeq2['doDESeq2'] == "T"</filter>
+    </data>
+    <data format="tabular" name="out_VOOM" label="${title}_topTable_VOOM.xls">
+         <filter>doVoom == "T"</filter>
+    </data>
+    <data format="html" name="html_file" label="${title}.html"/>
+  </outputs>
+ <stdio>
+     <exit_code range="4"   level="fatal"   description="Number of subject ids must match total number of samples in the input matrix" />
+ </stdio>
+ <tests>
+<test>
+<param name='input1' value='test_bams2mx.xls' ftype='tabular' />
+ <param name='treatment_name' value='liver' />
+ <param name='title' value='edgeRtest' />
+ <param name='useNDF' value='' />
+ <param name='doedgeR' value='T' />
+ <param name='doVoom' value='T' />
+ <param name='doDESeq2' value='T' />
+ <param name='fdrtype' value='fdr' />
+ <param name='edgeR_priordf' value="8" />
+ <param name='fdrthresh' value="0.05" />
+ <param name='control_name' value='heart' />
+ <param name='subjectids' value='' />
+ <param name='Control_cols' value='3,4,5,9' />
+ <param name='Treat_cols' value='2,6,7,8' />
+ <output name='out_edgeR' file='edgeRtest1out.xls' compare='diff' />
+ <output name='html_file' file='edgeRtest1out.html'  compare='diff' lines_diff='20' />
+</test>
+</tests>
+
+<configfiles>
+<configfile name="runme">
+<![CDATA[
+# 
+# edgeR.Rscript
+# updated npv 2011 for R 2.14.0 and edgeR 2.4.0 by ross
+# Performs DGE on a count table containing n replicates of two conditions
+#
+# Parameters
+#
+# 1 - Output Dir
+
+# Original edgeR code by: S.Lunke and A.Kaspi
+reallybig = log10(.Machine\$double.xmax)
+reallysmall = log10(.Machine\$double.xmin)
+library('stringr')
+library('gplots')
+library('edgeR')
+hmap2 = function(cmat,nsamp=100,outpdfname='heatmap2.pdf', TName='Treatment',group=NA,myTitle='title goes here')
+{
+# Perform clustering for significant pvalues after controlling FWER
+    samples = colnames(cmat)
+    gu = unique(group)
+    gn = rownames(cmat)
+    if (length(gu) == 2) {
+        col.map = function(g) {if (g==gu[1]) "#FF0000" else "#0000FF"}
+        pcols = unlist(lapply(group,col.map))        
+        } else {
+        colours = rainbow(length(gu),start=0,end=4/6)
+        pcols = colours[match(group,gu)]        }
+    dm = cmat[(! is.na(gn)),] 
+    # remove unlabelled hm rows
+    nprobes = nrow(dm)
+    # sub = paste('Showing',nprobes,'contigs ranked for evidence of differential abundance')
+    if (nprobes > nsamp) {
+      dm =dm[1:nsamp,]
+      #sub = paste('Showing',nsamp,'contigs ranked for evidence for differential abundance out of',nprobes,'total')
+    }
+    newcolnames = substr(colnames(dm),1,20)
+    colnames(dm) = newcolnames
+    pdf(outpdfname)
+    heatmap.2(dm,main=myTitle,ColSideColors=pcols,col=topo.colors(100),dendrogram="col",key=T,density.info='none',
+         Rowv=F,scale='row',trace='none',margins=c(8,8),cexRow=0.4,cexCol=0.5)
+    dev.off()
+}
+
+hmap = function(cmat,nmeans=4,outpdfname="heatMap.pdf",nsamp=250,TName='Treatment',group=NA,myTitle="Title goes here")
+{
+    # for 2 groups only was
+    #col.map = function(g) {if (g==TName) "#FF0000" else "#0000FF"}
+    #pcols = unlist(lapply(group,col.map))
+    gu = unique(group)
+    colours = rainbow(length(gu),start=0.3,end=0.6)
+    pcols = colours[match(group,gu)]
+    nrows = nrow(cmat)
+    mtitle = paste(myTitle,'Heatmap: n contigs =',nrows)
+    if (nrows > nsamp)  {
+               cmat = cmat[c(1:nsamp),]
+               mtitle = paste('Heatmap: Top ',nsamp,' DE contigs (of ',nrows,')',sep='')
+          }
+    newcolnames = substr(colnames(cmat),1,20)
+    colnames(cmat) = newcolnames
+    pdf(outpdfname)
+    heatmap(cmat,scale='row',main=mtitle,cexRow=0.3,cexCol=0.4,Rowv=NA,ColSideColors=pcols)
+    dev.off()
+}
+
+qqPlot = function(descr='qqplot',pvector, outpdf='qqplot.pdf',...)
+# stolen from https://gist.github.com/703512
+{
+    o = -log10(sort(pvector,decreasing=F))
+    e = -log10( 1:length(o)/length(o) )
+    o[o==-Inf] = reallysmall
+    o[o==Inf] = reallybig
+    maint = descr
+    pdf(outpdf)
+    plot(e,o,pch=19,cex=1, main=maint, ...,
+        xlab=expression(Expected~~-log[10](italic(p))),
+        ylab=expression(Observed~~-log[10](italic(p))),
+        xlim=c(0,max(e)), ylim=c(0,max(o)))
+    lines(e,e,col="red")
+    grid(col = "lightgray", lty = "dotted")
+    dev.off()
+}
+
+smearPlot = function(DGEList,deTags, outSmear, outMain)
+        {
+        pdf(outSmear)
+        plotSmear(DGEList,de.tags=deTags,main=outMain)
+        grid(col="lightgray", lty="dotted")
+        dev.off()
+        }
+        
+boxPlot = function(rawrs,cleanrs,maint,myTitle,pdfname)
+{   # 
+        nc = ncol(rawrs)
+        for (i in c(1:nc)) {rawrs[(rawrs[,i] < 0),i] = NA}
+        fullnames = colnames(rawrs)
+        newcolnames = substr(colnames(rawrs),1,20)
+        colnames(rawrs) = newcolnames
+        newcolnames = substr(colnames(cleanrs),1,20)
+        colnames(cleanrs) = newcolnames
+        defpar = par(no.readonly=T)
+        print.noquote('raw contig counts by sample:')
+        print.noquote(summary(rawrs))
+        print.noquote('normalised contig counts by sample:')
+        print.noquote(summary(cleanrs))
+        pdf(pdfname)
+        par(mfrow=c(1,2))
+        boxplot(rawrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('Raw:',maint))
+        grid(col="lightgray",lty="dotted")
+        boxplot(cleanrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('After ',maint))
+        grid(col="lightgray",lty="dotted")
+        dev.off()
+        pdfname = "sample_counts_histogram.pdf" 
+        nc = ncol(rawrs)
+        print.noquote(paste('Using ncol rawrs=',nc))
+        ncroot = round(sqrt(nc))
+        if (ncroot*ncroot < nc) { ncroot = ncroot + 1 }
+        m = c()
+        for (i in c(1:nc)) {
+              rhist = hist(rawrs[,i],breaks=100,plot=F)
+              m = append(m,max(rhist\$counts))
+             }
+        ymax = max(m)
+        ncols = length(fullnames)
+        if (ncols > 20) 
+        {
+           scale = 7*ncols/20
+           pdf(pdfname,width=scale,height=scale)
+        } else { 
+           pdf(pdfname)
+        }
+        par(mfrow=c(ncroot,ncroot))
+        for (i in c(1:nc)) {
+                 hist(rawrs[,i], main=paste("Contig logcount",i), xlab='log raw count', col="maroon", 
+                 breaks=100,sub=fullnames[i],cex=0.8,ylim=c(0,ymax))
+             }
+        dev.off()
+        par(defpar)
+      
+}
+
+cumPlot = function(rawrs,cleanrs,maint,myTitle)
+{   # updated to use ecdf
+        pdfname = "Filtering_rowsum_bar_charts.pdf"
+        defpar = par(no.readonly=T)
+        lrs = log(rawrs,10) 
+        lim = max(lrs)
+        pdf(pdfname)
+        par(mfrow=c(2,1))
+        hist(lrs,breaks=100,main=paste('Before:',maint),xlab="# Reads (log)",
+             ylab="Count",col="maroon",sub=myTitle, xlim=c(0,lim),las=1)
+        grid(col="lightgray", lty="dotted")
+        lrs = log(cleanrs,10) 
+        hist(lrs,breaks=100,main=paste('After:',maint),xlab="# Reads (log)",
+             ylab="Count",col="maroon",sub=myTitle,xlim=c(0,lim),las=1)
+        grid(col="lightgray", lty="dotted")
+        dev.off()
+        par(defpar)
+}
+
+cumPlot1 = function(rawrs,cleanrs,maint,myTitle)
+{   # updated to use ecdf
+        pdfname = paste(gsub(" ","", myTitle , fixed=TRUE),"RowsumCum.pdf",sep='_')
+        pdf(pdfname)
+        par(mfrow=c(2,1))
+        lastx = max(rawrs)
+        rawe = knots(ecdf(rawrs))
+        cleane = knots(ecdf(cleanrs))
+        cy = 1:length(cleane)/length(cleane)
+        ry = 1:length(rawe)/length(rawe)
+        plot(rawe,ry,type='l',main=paste('Before',maint),xlab="Log Contig Total Reads",
+             ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle)
+        grid(col="blue")
+        plot(cleane,cy,type='l',main=paste('After',maint),xlab="Log Contig Total Reads",
+             ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle)
+        grid(col="blue")
+        dev.off()
+}
+
+
+
+doGSEAold = function(y=NULL,design=NULL,histgmt="",
+                  bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
+                  ntest=0, myTitle="myTitle", outfname="GSEA.xls", minnin=5, maxnin=2000,fdrthresh=0.05,fdrtype="BH")
+{
+  sink('Camera.log')
+  genesets = c()
+  if (bigmt > "")
+  {
+    bigenesets = readLines(bigmt)
+    genesets = bigenesets
+  }
+  if (histgmt > "")
+  {
+    hgenesets = readLines(histgmt)
+    if (bigmt > "") {
+      genesets = rbind(genesets,hgenesets)
+    } else {
+      genesets = hgenesets
+    } # use only history if no bi
+  }
+  print.noquote(paste("@@@read",length(genesets), 'genesets from',histgmt,bigmt))
+  genesets = strsplit(genesets,'\t') # tabular. genesetid\tURLorwhatever\tgene_1\t..\tgene_n
+  outf = outfname
+  head=paste(myTitle,'edgeR GSEA')
+  write(head,file=outfname,append=F)
+  ntest=length(genesets)
+  urownames = toupper(rownames(y))
+  upcam = c()
+  downcam = c()
+  for (i in 1:ntest) {
+    gs = unlist(genesets[i])
+    g = gs[1] # geneset_id
+    u = gs[2]
+    if (u > "") { u = paste("<a href=\'",u,"\'>",u,"</a>",sep="") }
+    glist = gs[3:length(gs)] # member gene symbols
+    glist = toupper(glist)
+    inglist = urownames %in% glist
+    nin = sum(inglist)
+    if ((nin > minnin) && (nin < maxnin)) {
+      ### print(paste('@@found',sum(inglist),'genes in glist'))
+      camres = camera(y=y,index=inglist,design=design)
+      if (! is.null(camres)) {
+      rownames(camres) = g # gene set name
+      camres = cbind(GeneSet=g,URL=u,camres)
+      if (camres\$Direction == "Up") 
+        {
+        upcam = rbind(upcam,camres) } else {
+          downcam = rbind(downcam,camres)
+        }
+      }
+   }
+  }
+  uscam = upcam[order(upcam\$PValue),]
+  unadjp = uscam\$PValue
+  uscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
+  nup = max(10,sum((uscam\$adjPValue < fdrthresh)))
+  dscam = downcam[order(downcam\$PValue),]
+  unadjp = dscam\$PValue
+  dscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
+  ndown = max(10,sum((dscam\$adjPValue < fdrthresh)))
+  write.table(uscam,file=paste('camera_up',outfname,sep='_'),quote=F,sep='\t',row.names=F)
+  write.table(dscam,file=paste('camera_down',outfname,sep='_'),quote=F,sep='\t',row.names=F)
+  print.noquote(paste('@@@@@ Camera up top',nup,'gene sets:'))
+  write.table(head(uscam,nup),file="",quote=F,sep='\t',row.names=F)
+  print.noquote(paste('@@@@@ Camera down top',ndown,'gene sets:'))
+  write.table(head(dscam,ndown),file="",quote=F,sep='\t',row.names=F)
+  sink()
+}
+
+
+
+
+doGSEA = function(y=NULL,design=NULL,histgmt="",
+                  bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
+                  ntest=0, myTitle="myTitle", outfname="GSEA.xls", minnin=5, maxnin=2000,fdrthresh=0.05,fdrtype="BH")
+{
+  sink('Camera.log')
+  genesets = c()
+  if (bigmt > "")
+  {
+    bigenesets = readLines(bigmt)
+    genesets = bigenesets
+  }
+  if (histgmt > "")
+  {
+    hgenesets = readLines(histgmt)
+    if (bigmt > "") {
+      genesets = rbind(genesets,hgenesets)
+    } else {
+      genesets = hgenesets
+    } # use only history if no bi
+  }
+  print.noquote(paste("@@@read",length(genesets), 'genesets from',histgmt,bigmt))
+  genesets = strsplit(genesets,'\t') # tabular. genesetid\tURLorwhatever\tgene_1\t..\tgene_n
+  outf = outfname
+  head=paste(myTitle,'edgeR GSEA')
+  write(head,file=outfname,append=F)
+  ntest=length(genesets)
+  urownames = toupper(rownames(y))
+  upcam = c()
+  downcam = c()
+  incam = c()
+  urls = c()
+  gsids = c()
+  for (i in 1:ntest) {
+    gs = unlist(genesets[i])
+    gsid = gs[1] # geneset_id
+    url = gs[2]
+    if (url > "") { url = paste("<a href=\'",url,"\'>",url,"</a>",sep="") }
+    glist = gs[3:length(gs)] # member gene symbols
+    glist = toupper(glist)
+    inglist = urownames %in% glist
+    nin = sum(inglist)
+    if ((nin > minnin) && (nin < maxnin)) {
+      incam = c(incam,inglist)
+      gsids = c(gsids,gsid)
+      urls = c(urls,url)
+    }
+  }
+  incam = as.list(incam)
+  names(incam) = gsids
+  allcam = camera(y=y,index=incam,design=design)
+  allcamres = cbind(geneset=gsids,allcam,URL=urls)
+  for (i in 1:ntest) {
+    camres = allcamres[i]
+    res = try(test = (camres\$Direction == "Up"))
+    if ("try-error" %in% class(res)) {
+      cat("test failed, camres = :")
+      print.noquote(camres)
+    } else  { if (camres\$Direction == "Up")
+    {  upcam = rbind(upcam,camres)
+    } else { downcam = rbind(downcam,camres)
+    }
+              
+    }
+  }
+  uscam = upcam[order(upcam\$PValue),]
+  unadjp = uscam\$PValue
+  uscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
+  nup = max(10,sum((uscam\$adjPValue < fdrthresh)))
+  dscam = downcam[order(downcam\$PValue),]
+  unadjp = dscam\$PValue
+  dscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
+  ndown = max(10,sum((dscam\$adjPValue < fdrthresh)))
+  write.table(uscam,file=paste('camera_up',outfname,sep='_'),quote=F,sep='\t',row.names=F)
+  write.table(dscam,file=paste('camera_down',outfname,sep='_'),quote=F,sep='\t',row.names=F)
+  print.noquote(paste('@@@@@ Camera up top',nup,'gene sets:'))
+  write.table(head(uscam,nup),file="",quote=F,sep='\t',row.names=F)
+  print.noquote(paste('@@@@@ Camera down top',ndown,'gene sets:'))
+  write.table(head(dscam,ndown),file="",quote=F,sep='\t',row.names=F)
+  sink()
+  }
+ 
+
+edgeIt = function (Count_Matrix=c(),group=c(),out_edgeR=F,out_VOOM=F,out_DESeq2=F,fdrtype='fdr',priordf=5, 
+        fdrthresh=0.05,outputdir='.', myTitle='Differential Counts',libSize=c(),useNDF=F,
+        filterquantile=0.2, subjects=c(),mydesign=NULL,
+        doDESeq2=T,doVoom=T,doCamera=T,doedgeR=T,org='hg19',
+        histgmt="", bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
+        doCook=F,DESeq_fitType="parameteric") 
+{
+  # Error handling
+  if (length(unique(group))!=2){
+    print("Number of conditions identified in experiment does not equal 2")
+    q()
+    }
+  require(edgeR)
+  options(width = 512) 
+  mt = paste(unlist(strsplit(myTitle,'_')),collapse=" ")
+  allN = nrow(Count_Matrix)
+  nscut = round(ncol(Count_Matrix)/2)
+  colTotmillionreads = colSums(Count_Matrix)/1e6
+  counts.dataframe = as.data.frame(c()) 
+  rawrs = rowSums(Count_Matrix)
+  nonzerod = Count_Matrix[(rawrs > 0),] # remove all zero count genes
+  nzN = nrow(nonzerod)
+  nzrs = rowSums(nonzerod)
+  zN = allN - nzN
+  print('# Quantiles for non-zero row counts:',quote=F)
+  print(quantile(nzrs,probs=seq(0,1,0.1)),quote=F)
+  if (useNDF == T)
+  {
+    gt1rpin3 = rowSums(Count_Matrix/expandAsMatrix(colTotmillionreads,dim(Count_Matrix)) >= 1) >= nscut
+    lo = colSums(Count_Matrix[!gt1rpin3,])
+    workCM = Count_Matrix[gt1rpin3,]
+    cleanrs = rowSums(workCM)
+    cleanN = length(cleanrs)
+    meth = paste( "After removing",length(lo),"contigs with fewer than ",nscut," sample read counts >= 1 per million, there are",sep="")
+    print(paste("Read",allN,"contigs. Removed",zN,"contigs with no reads.",meth,cleanN,"contigs"),quote=F)
+    maint = paste('Filter >=1/million reads in >=',nscut,'samples')
+  }   else {        
+    useme = (nzrs > quantile(nzrs,filterquantile))
+    workCM = nonzerod[useme,]
+    lo = colSums(nonzerod[!useme,])
+    cleanrs = rowSums(workCM)
+    cleanN = length(cleanrs)
+    meth = paste("After filtering at count quantile =",filterquantile,", there are",sep="")
+    print(paste('Read',allN,"contigs. Removed",zN,"with no reads.",meth,cleanN,"contigs"),quote=F)
+    maint = paste('Filter below',filterquantile,'quantile')
+  }
+  cumPlot(rawrs=rawrs,cleanrs=cleanrs,maint=maint,myTitle=myTitle)
+  allgenes = rownames(workCM)
+  reg = "^chr([0-9]+):([0-9]+)-([0-9]+)"
+  genecards="<a href=\'http://www.genecards.org/index.php?path=/Search/keyword/"
+  ucsc = paste("<a href=\'http://genome.ucsc.edu/cgi-bin/hgTracks?db=",org,sep='')
+  testreg = str_match(allgenes,reg)
+  if (sum(!is.na(testreg[,1]))/length(testreg[,1]) > 0.8) # is ucsc style string
+  {
+    print("@@ using ucsc substitution for urls")
+    contigurls = paste0(ucsc,"&amp;position=chr",testreg[,2],":",testreg[,3],"-",testreg[,4],"\'>",allgenes,"</a>")
+  } else {
+    print("@@ using genecards substitution for urls")
+    contigurls = paste0(genecards,allgenes,"\'>",allgenes,"</a>")
+  }
+  print.noquote("# urls")
+  print.noquote(head(contigurls))
+  print(paste("# Total low count contigs per sample = ",paste(lo,collapse=',')),quote=F) 
+  cmrowsums = rowSums(workCM)
+  TName=unique(group)[1]
+  CName=unique(group)[2]
+  if (is.null(mydesign)) {
+    if (length(subjects) == 0) 
+    {
+      mydesign = model.matrix(~group)
+    } 
+    else { 
+      subjf = factor(subjects)
+      mydesign = model.matrix(~subjf+group) # we block on subject so make group last to simplify finding it
+    }
+  } 
+  print.noquote(paste('Using samples:',paste(colnames(workCM),collapse=',')))
+  print.noquote('Using design matrix:')
+  print.noquote(mydesign)
+  if (doedgeR) {
+  sink('edgeR.log')
+  #### Setup DGEList object
+  DGEList = DGEList(counts=workCM, group = group)
+  DGEList = calcNormFactors(DGEList)
+
+  DGEList = estimateGLMCommonDisp(DGEList,mydesign)
+  comdisp = DGEList\$common.dispersion
+  DGEList = estimateGLMTrendedDisp(DGEList,mydesign)
+  if (edgeR_priordf > 0) {
+    print.noquote(paste("prior.df =",edgeR_priordf))
+    DGEList = estimateGLMTagwiseDisp(DGEList,mydesign,prior.df = edgeR_priordf)
+  } else {
+    DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
+  }
+  DGLM = glmFit(DGEList,design=mydesign)
+  DE = glmLRT(DGLM,coef=ncol(DGLM\$design)) # always last one - subject is first if needed
+  efflib = DGEList\$samples\$lib.size*DGEList\$samples\$norm.factors
+  normData = (1e+06*DGEList\$counts/efflib)
+  uoutput = cbind( 
+    Name=as.character(rownames(DGEList\$counts)),
+    DE\$table,
+    adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
+    Dispersion=DGEList\$tagwise.dispersion,totreads=cmrowsums,normData,
+    DGEList\$counts
+  )
+  soutput = uoutput[order(DE\$table\$PValue),] # sorted into p value order - for quick toptable
+  goodness = gof(DGLM, pcutoff=fdrthresh)
+  if (sum(goodness\$outlier) > 0) {
+    print.noquote('GLM outliers:')
+    print(paste(rownames(DGLM)[(goodness\$outlier)],collapse=','),quote=F)
+    } else { 
+      print('No GLM fit outlier genes found\n')
+    }
+  z = limma::zscoreGamma(goodness\$gof.statistic, shape=goodness\$df/2, scale=2)
+  pdf("edgeR_GoodnessofFit.pdf")
+  qq = qqnorm(z, panel.first=grid(), main="tagwise dispersion")
+  abline(0,1,lwd=3)
+  points(qq\$x[goodness\$outlier],qq\$y[goodness\$outlier], pch=16, col="maroon")
+  dev.off()
+  estpriorn = getPriorN(DGEList)
+  print(paste("Common Dispersion =",comdisp,"CV = ",sqrt(comdisp),"getPriorN = ",estpriorn),quote=F)
+  efflib = DGEList\$samples\$lib.size*DGEList\$samples\$norm.factors
+  normData = (1e+06*DGEList\$counts/efflib)
+  uniqueg = unique(group)
+  #### Plot MDS
+  sample_colors =  match(group,levels(group))
+  sampleTypes = levels(factor(group))
+  print.noquote(sampleTypes)
+  pdf("edgeR_MDSplot.pdf")
+  plotMDS.DGEList(DGEList,main=paste("edgeR MDS for",myTitle),cex=0.5,col=sample_colors,pch=sample_colors)
+  legend(x="topleft", legend = sampleTypes,col=c(1:length(sampleTypes)), pch=19)
+  grid(col="blue")
+  dev.off()
+  colnames(normData) = paste( colnames(normData),'N',sep="_")
+  print(paste('Raw sample read totals',paste(colSums(nonzerod,na.rm=T),collapse=',')))
+  nzd = data.frame(log(nonzerod + 1e-2,10))
+  try( boxPlot(rawrs=nzd,cleanrs=log(normData,10),maint='TMM Normalisation',myTitle=myTitle,pdfname="edgeR_raw_norm_counts_box.pdf") )
+  write.table(soutput,file=out_edgeR, quote=FALSE, sep="\t",row.names=F)
+  tt = cbind( 
+    Name=as.character(rownames(DGEList\$counts)),
+    DE\$table,
+    adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
+    Dispersion=DGEList\$tagwise.dispersion,totreads=cmrowsums
+  )
+  print.noquote("# edgeR Top tags\n")
+  tt = cbind(tt,URL=contigurls) # add to end so table isn't laid out strangely
+  tt = tt[order(DE\$table\$PValue),] 
+  print.noquote(tt[1:50,])
+  deTags = rownames(uoutput[uoutput\$adj.p.value < fdrthresh,])
+  nsig = length(deTags)
+  print(paste('#',nsig,'tags significant at adj p=',fdrthresh),quote=F)
+  deColours = ifelse(deTags,'red','black')
+  pdf("edgeR_BCV_vs_abundance.pdf")
+  plotBCV(DGEList, cex=0.3, main="Biological CV vs abundance")
+  dev.off()
+  dg = DGEList[order(DE\$table\$PValue),]
+  #normData = (1e+06 * dg\$counts/expandAsMatrix(dg\$samples\$lib.size, dim(dg)))
+  efflib = dg\$samples\$lib.size*dg\$samples\$norm.factors
+  normData = (1e+06*dg\$counts/efflib)
+  outpdfname="edgeR_top_100_heatmap.pdf"
+  hmap2(normData,nsamp=100,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste('edgeR Heatmap',myTitle))
+  outSmear = "edgeR_smearplot.pdf"
+  outMain = paste("Smear Plot for ",TName,' Vs ',CName,' (FDR@',fdrthresh,' N = ',nsig,')',sep='')
+  smearPlot(DGEList=DGEList,deTags=deTags, outSmear=outSmear, outMain = outMain)
+  qqPlot(descr=paste(myTitle,'edgeR adj p QQ plot'),pvector=tt\$adj.p.value,outpdf='edgeR_qqplot.pdf')
+  norm.factor = DGEList\$samples\$norm.factors
+  topresults.edgeR = soutput[which(soutput\$adj.p.value < fdrthresh), ]
+  edgeRcountsindex = which(allgenes %in% rownames(topresults.edgeR))
+  edgeRcounts = rep(0, length(allgenes))
+  edgeRcounts[edgeRcountsindex] = 1  # Create venn diagram of hits
+  sink()
+  } ### doedgeR
+  if (doDESeq2 == T)
+  {
+    sink("DESeq2.log")
+    # DESeq2
+    require('DESeq2')
+    library('RColorBrewer')
+    if (length(subjects) == 0)
+        {
+        pdata = data.frame(Name=colnames(workCM),Rx=group,row.names=colnames(workCM))
+        deSEQds = DESeqDataSetFromMatrix(countData = workCM,  colData = pdata, design = formula(~ Rx))
+        } else {
+        pdata = data.frame(Name=colnames(workCM),Rx=group,subjects=subjects,row.names=colnames(workCM))
+        deSEQds = DESeqDataSetFromMatrix(countData = workCM,  colData = pdata, design = formula(~ subjects + Rx))
+        }
+    #DESeq2 = DESeq(deSEQds,fitType='local',pAdjustMethod=fdrtype)
+    #rDESeq = results(DESeq2)
+    #newCountDataSet(workCM, group)
+    deSeqDatsizefac = estimateSizeFactors(deSEQds)
+    deSeqDatdisp = estimateDispersions(deSeqDatsizefac,fitType=DESeq_fitType)
+    resDESeq = nbinomWaldTest(deSeqDatdisp, pAdjustMethod=fdrtype)
+    rDESeq = as.data.frame(results(resDESeq))
+    rDESeq = cbind(Contig=rownames(workCM),rDESeq,NReads=cmrowsums,URL=contigurls)
+    srDESeq = rDESeq[order(rDESeq\$pvalue),]
+    qqPlot(descr=paste(myTitle,'DESeq2 adj p qq plot'),pvector=rDESeq\$padj,outpdf='DESeq2_qqplot.pdf')
+    cat("# DESeq top 50\n")
+    print.noquote(srDESeq[1:50,])
+    write.table(srDESeq,file=out_DESeq2, quote=FALSE, sep="\t",row.names=F)
+    topresults.DESeq = rDESeq[which(rDESeq\$padj < fdrthresh), ]
+    DESeqcountsindex = which(allgenes %in% rownames(topresults.DESeq))
+    DESeqcounts = rep(0, length(allgenes))
+    DESeqcounts[DESeqcountsindex] = 1
+    pdf("DESeq2_dispersion_estimates.pdf")
+    plotDispEsts(resDESeq)
+    dev.off()
+    ysmall = abs(min(rDESeq\$log2FoldChange))
+    ybig = abs(max(rDESeq\$log2FoldChange))
+    ylimit = min(4,ysmall,ybig)
+    pdf("DESeq2_MA_plot.pdf")
+    plotMA(resDESeq,main=paste(myTitle,"DESeq2 MA plot"),ylim=c(-ylimit,ylimit))
+    dev.off()
+    rlogres = rlogTransformation(resDESeq)
+    sampledists = dist( t( assay(rlogres) ) )
+    sdmat = as.matrix(sampledists)
+    pdf("DESeq2_sample_distance_plot.pdf")
+    heatmap.2(sdmat,trace="none",main=paste(myTitle,"DESeq2 sample distances"),
+         col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255))
+    dev.off()
+    ###outpdfname="DESeq2_top50_heatmap.pdf"
+    ###hmap2(sresDESeq,nsamp=50,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste('DESeq2 vst rlog Heatmap',myTitle))
+    sink()
+    result = try( (ppca = plotPCA( varianceStabilizingTransformation(deSeqDatdisp,blind=T), intgroup=c("Rx","Name")) ) )
+    if ("try-error" %in% class(result)) {
+         print.noquote('DESeq2 plotPCA failed.')
+         } else {
+         pdf("DESeq2_PCA_plot.pdf")
+         #### wtf - print? Seems needed to get this to work
+         print(ppca)
+         dev.off()
+        }
+  }
+
+  if (doVoom == T) {
+      sink('VOOM.log')
+      if (doedgeR == F) {
+         #### Setup DGEList object
+         DGEList = DGEList(counts=workCM, group = group)
+         DGEList = calcNormFactors(DGEList)
+         DGEList = estimateGLMCommonDisp(DGEList,mydesign)
+         DGEList = estimateGLMTrendedDisp(DGEList,mydesign)
+         DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
+         DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
+         norm.factor = DGEList\$samples\$norm.factors
+         }
+      pdf("VOOM_mean_variance_plot.pdf")
+      dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = colSums(workCM) * norm.factor)
+      dev.off()
+      # Use limma to fit data
+      fit = lmFit(dat.voomed, mydesign)
+      fit = eBayes(fit)
+      rvoom = topTable(fit, coef = length(colnames(mydesign)), adj = fdrtype, n = Inf, sort="none")
+      qqPlot(descr=paste(myTitle,'VOOM-limma adj p QQ plot'),pvector=rvoom\$adj.P.Val,outpdf='VOOM_qqplot.pdf')
+      rownames(rvoom) = rownames(workCM)
+      rvoom = cbind(rvoom,NReads=cmrowsums,URL=contigurls)
+      srvoom = rvoom[order(rvoom\$P.Value),]
+      cat("# VOOM top 50\n")
+      print(srvoom[1:50,])
+      write.table(srvoom,file=out_VOOM, quote=FALSE, sep="\t",row.names=F)
+      # Use an FDR cutoff to find interesting samples for edgeR, DESeq and voom/limma
+      topresults.voom = rvoom[which(rvoom\$adj.P.Val < fdrthresh), ]
+      voomcountsindex = which(allgenes %in% topresults.voom\$ID)
+      voomcounts = rep(0, length(allgenes))
+      voomcounts[voomcountsindex] = 1
+      sink()
+  }
+
+  if (doCamera) {
+  doGSEA(y=DGEList,design=mydesign,histgmt=histgmt,bigmt=bigmt,ntest=20,myTitle=myTitle,
+    outfname=paste(mt,"GSEA.xls",sep="_"),fdrthresh=fdrthresh,fdrtype=fdrtype)
+  }
+
+  if ((doDESeq2==T) || (doVoom==T) || (doedgeR==T)) {
+    if ((doVoom==T) && (doDESeq2==T) && (doedgeR==T)) {
+        vennmain = paste(mt,'Voom,edgeR and DESeq2 overlap at FDR=',fdrthresh)
+        counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts, 
+                                       VOOM_limma = voomcounts, row.names = allgenes)
+       } else if ((doDESeq2==T) && (doedgeR==T))  {
+         vennmain = paste(mt,'DESeq2 and edgeR overlap at FDR=',fdrthresh)
+         counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts, row.names = allgenes)
+       } else if ((doVoom==T) && (doedgeR==T)) {
+        vennmain = paste(mt,'Voom and edgeR overlap at FDR=',fdrthresh)
+        counts.dataframe = data.frame(edgeR = edgeRcounts, VOOM_limma = voomcounts, row.names = allgenes)
+       }
+    
+    if (nrow(counts.dataframe > 1)) {
+      counts.venn = vennCounts(counts.dataframe)
+      vennf = "Venn_significant_genes_overlap.pdf" 
+      pdf(vennf)
+      vennDiagram(counts.venn,main=vennmain,col="maroon")
+      dev.off()
+    }
+  } #### doDESeq2 or doVoom
+  
+}
+#### Done
+
+###sink(stdout(),append=T,type="message")
+builtin_gmt = ""
+history_gmt = ""
+history_gmt_name = ""
+out_edgeR = F
+out_DESeq2 = F
+out_VOOM = "$out_VOOM"
+doDESeq2 = $DESeq2.doDESeq2 # make these T or F
+doVoom = $doVoom
+doCamera = F
+doedgeR = $edgeR.doedgeR
+edgeR_priordf = 0
+
+
+#if $doVoom == "T":
+  out_VOOM = "$out_VOOM"
+#end if
+
+#if $DESeq2.doDESeq2 == "T":
+  out_DESeq2 = "$out_DESeq2"
+  DESeq_fitType = "$DESeq2.DESeq_fitType"
+#end if
+
+#if $edgeR.doedgeR == "T":
+  out_edgeR = "$out_edgeR"
+  edgeR_priordf = $edgeR.edgeR_priordf  
+#end if
+
+<!--
+#if $camera.doCamera == 'T'
+ doCamera = $camera.doCamera
+ #if $camera.gmtSource.refgmtSource == "indexed" or $camera.gmtSource.refgmtSource == "both":
+  builtin_gmt = "${camera.gmtSource.builtinGMT.fields.path}"
+ #end if
+ #if $camera.gmtSource.refgmtSource == "history" or $camera.gmtSource.refgmtSource == "both":
+    history_gmt = "${camera.gmtSource.ownGMT}"
+    history_gmt_name = "${camera.gmtSource.ownGMT.name}"
+  #end if
+#end if
+-->
+
+if (sum(c(doedgeR,doVoom,doDESeq2)) == 0)
+{
+write("No methods chosen - nothing to do! Please try again after choosing one or more methods", stderr())
+quit(save="no",status=2)
+}
+
+Out_Dir = "$html_file.files_path"
+Input =  "$input1"
+TreatmentName = "$treatment_name"
+TreatmentCols = "$Treat_cols"
+ControlName = "$control_name"
+ControlCols= "$Control_cols"
+org = "$input1.dbkey"
+if (org == "") { org = "hg19"}
+fdrtype = "$fdrtype"
+fdrthresh = $fdrthresh
+useNDF = $useNDF
+fQ = $fQ # non-differential centile cutoff
+myTitle = "$title"
+sids = strsplit("$subjectids",',')
+subjects = unlist(sids)
+nsubj = length(subjects)
+TCols = as.numeric(strsplit(TreatmentCols,",")[[1]])-1
+CCols = as.numeric(strsplit(ControlCols,",")[[1]])-1 
+cat('Got TCols=')
+cat(TCols)
+cat('; CCols=')
+cat(CCols)
+cat('\n')
+useCols = c(TCols,CCols)
+if (file.exists(Out_Dir) == F) dir.create(Out_Dir)
+Count_Matrix = read.table(Input,header=T,row.names=1,sep='\t') #Load tab file assume header
+snames = colnames(Count_Matrix)
+nsamples = length(snames)
+if (nsubj >  0 & nsubj != nsamples) {
+options("show.error.messages"=T)
+mess = paste('Fatal error: Supplied subject id list',paste(subjects,collapse=','),
+   'has length',nsubj,'but there are',nsamples,'samples',paste(snames,collapse=','))
+write(mess, stderr())
+quit(save="no",status=4)
+}
+if (length(subjects) != 0) {subjects = subjects[useCols]}
+Count_Matrix = Count_Matrix[,useCols] ### reorder columns
+rn = rownames(Count_Matrix)
+islib = rn %in% c('librarySize','NotInBedRegions')
+LibSizes = Count_Matrix[subset(rn,islib),][1] # take first
+Count_Matrix = Count_Matrix[subset(rn,! islib),]
+group = c(rep(TreatmentName,length(TCols)), rep(ControlName,length(CCols)) )             #Build a group descriptor
+group = factor(group, levels=c(ControlName,TreatmentName))
+colnames(Count_Matrix) = paste(group,colnames(Count_Matrix),sep="_")                   #Relable columns
+results = edgeIt(Count_Matrix=Count_Matrix,group=group, out_edgeR=out_edgeR, out_VOOM=out_VOOM, out_DESeq2=out_DESeq2,
+                 fdrtype='BH',mydesign=NULL,priordf=edgeR_priordf,fdrthresh=fdrthresh,outputdir='.',
+                 myTitle=myTitle,useNDF=F,libSize=c(),filterquantile=fQ,subjects=subjects,
+                 doDESeq2=doDESeq2,doVoom=doVoom,doCamera=doCamera,doedgeR=doedgeR,org=org,
+                 histgmt=history_gmt,bigmt=builtin_gmt,DESeq_fitType=DESeq_fitType)
+sessionInfo()
+]]>
+</configfile>
+</configfiles>
+<help>
+
+**What it does**
+
+Allows short read sequence counts from controlled experiments to be analysed for differentially expressed genes.
+Optionally adds a term for subject if not all samples are independent or if some other factor needs to be blocked in the design.
+
+**Input**
+
+Requires a count matrix as a tabular file. These are best made using the companion HTSeq_ based counter Galaxy wrapper
+and your fave gene model to generate inputs. Each row is a genomic feature (gene or exon eg) and each column the 
+non-negative integer count of reads from one sample overlapping the feature. 
+The matrix must have a header row uniquely identifying the source samples, and unique row names in 
+the first column. Typically the row names are gene symbols or probe ids for downstream use in GSEA and other methods.
+
+**Specifying comparisons**
+
+This is basically dumbed down for two factors - case vs control.
+
+More complex interfaces are possible but painful at present. 
+Probably need to specify a phenotype file to do this better.
+Work in progress. Send code.
+
+If you have (eg) paired samples and wish to include a term in the GLM to account for some other factor (subject in the case of paired samples),
+put a comma separated list of indicators for every sample (whether modelled or not!) indicating (eg) the subject number or 
+A list of integers, one for each subject or an empty string if samples are all independent.
+If not empty, there must be exactly as many integers in the supplied integer list as there are columns (samples) in the count matrix.
+Integers for samples that are not in the analysis *must* be present in the string as filler even if not used.
+
+So if you have 2 pairs out of 6 samples, you need to put in unique integers for the unpaired ones
+eg if you had 6 samples with the first two independent but the second and third pairs each being from independent subjects. you might use
+8,9,1,1,2,2 
+as subject IDs to indicate two paired samples from the same subject in columns 3/4 and 5/6
+
+**Methods available**
+
+You can run 3 popular Bioconductor packages available for count data.
+
+edgeR - see edgeR_ for details
+
+VOOM/limma - see limma_VOOM_ for details
+
+DESeq2 - see DESeq2_ for details
+
+and optionally camera in edgeR which works better if MSigDB is installed.
+
+**Outputs**
+
+Some helpful plots and analysis results. Note that most of these are produced using R code 
+suggested by the excellent documentation and vignettes for the Bioconductor
+packages invoked. The Tool Factory is used to automatically lay these out for you to enjoy.
+
+**Note on Voom**
+
+The voom from limma version 3.16.6 help in R includes this from the authors - but you should read the paper to interpret this method.
+
+This function is intended to process RNA-Seq or ChIP-Seq data prior to linear modelling in limma.
+
+voom is an acronym for mean-variance modelling at the observational level.
+The key concern is to estimate the mean-variance relationship in the data, then use this to compute appropriate weights for each observation.
+Count data almost show non-trivial mean-variance relationships. Raw counts show increasing variance with increasing count size, while log-counts typically show a decreasing mean-variance trend.
+This function estimates the mean-variance trend for log-counts, then assigns a weight to each observation based on its predicted variance.
+The weights are then used in the linear modelling process to adjust for heteroscedasticity.
+
+In an experiment, a count value is observed for each tag in each sample. A tag-wise mean-variance trend is computed using lowess.
+The tag-wise mean is the mean log2 count with an offset of 0.5, across samples for a given tag.
+The tag-wise variance is the quarter-root-variance of normalized log2 counts per million values with an offset of 0.5, across samples for a given tag.
+Tags with zero counts across all samples are not included in the lowess fit. Optional normalization is performed using normalizeBetweenArrays.
+Using fitted values of log2 counts from a linear model fit by lmFit, variances from the mean-variance trend were interpolated for each observation.
+This was carried out by approxfun. Inverse variance weights can be used to correct for mean-variance trend in the count data.
+
+
+Author(s)
+
+Charity Law and Gordon Smyth
+
+References
+
+Law, CW (2013). Precision weights for gene expression analysis. PhD Thesis. University of Melbourne, Australia.
+
+Law, CW, Chen, Y, Shi, W, Smyth, GK (2013). Voom! Precision weights unlock linear model analysis tools for RNA-seq read counts.
+Technical Report 1 May 2013, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Reseach, Melbourne, Australia.
+http://www.statsci.org/smyth/pubs/VoomPreprint.pdf
+
+See Also
+
+A voom case study is given in the edgeR User's Guide.
+
+vooma is a similar function but for microarrays instead of RNA-seq.
+
+
+***old rant on changes to Bioconductor package variable names between versions***
+
+The edgeR authors made a small cosmetic change in the name of one important variable (from p.value to PValue) 
+breaking this and all other code that assumed the old name for this variable, 
+between edgeR2.4.4 and 2.4.6 (the version for R 2.14 as at the time of writing). 
+This means that all code using edgeR is sensitive to the version. I think this was a very unwise thing 
+to do because it wasted hours of my time to track down and will similarly cost other edgeR users dearly
+when their old scripts break. This tool currently now works with 2.4.6.
+
+**Note on prior.N**
+
+http://seqanswers.com/forums/showthread.php?t=5591 says:
+
+*prior.n*
+
+The value for prior.n determines the amount of smoothing of tagwise dispersions towards the common dispersion. 
+You can think of it as like a "weight" for the common value. (It is actually the weight for the common likelihood 
+in the weighted likelihood equation). The larger the value for prior.n, the more smoothing, i.e. the closer your 
+tagwise dispersion estimates will be to the common dispersion. If you use a prior.n of 1, then that gives the 
+common likelihood the weight of one observation.
+
+In answer to your question, it is a good thing to squeeze the tagwise dispersions towards a common value, 
+or else you will be using very unreliable estimates of the dispersion. I would not recommend using the value that 
+you obtained from estimateSmoothing()---this is far too small and would result in virtually no moderation 
+(squeezing) of the tagwise dispersions. How many samples do you have in your experiment? 
+What is the experimental design? If you have few samples (less than 6) then I would suggest a prior.n of at least 10. 
+If you have more samples, then the tagwise dispersion estimates will be more reliable, 
+so you could consider using a smaller prior.n, although I would hesitate to use a prior.n less than 5. 
+
+
+From Bioconductor Digest, Vol 118, Issue 5, Gordon writes:
+
+Dear Dorota,
+
+The important settings are prior.df and trend.
+
+prior.n and prior.df are related through prior.df = prior.n * residual.df,
+and your experiment has residual.df = 36 - 12 = 24.  So the old setting of
+prior.n=10 is equivalent for your data to prior.df = 240, a very large
+value.  Going the other way, the new setting of prior.df=10 is equivalent
+to prior.n=10/24.
+
+To recover old results with the current software you would use
+
+  estimateTagwiseDisp(object, prior.df=240, trend="none")
+
+To get the new default from old software you would use
+
+  estimateTagwiseDisp(object, prior.n=10/24, trend=TRUE)
+
+Actually the old trend method is equivalent to trend="loess" in the new
+software. You should use plotBCV(object) to see whether a trend is
+required.
+
+Note you could also use
+
+  prior.n = getPriorN(object, prior.df=10)
+
+to map between prior.df and prior.n.
+
+----
+
+**Attributions**
+
+edgeR - edgeR_ 
+
+VOOM/limma - limma_VOOM_ 
+
+DESeq2 - DESeq2_ for details
+
+See above for Bioconductor package documentation for packages exposed in Galaxy by this tool and app store package.
+
+Galaxy_ (that's what you are using right now!) for gluing everything together 
+
+Otherwise, all code and documentation comprising this tool was written by Ross Lazarus and is 
+licensed to you under the LGPL_ like other rgenetics artefacts
+
+.. _LGPL: http://www.gnu.org/copyleft/lesser.html
+.. _HTSeq: http://www-huber.embl.de/users/anders/HTSeq/doc/index.html
+.. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
+.. _DESeq2: http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
+.. _limma_VOOM: http://www.bioconductor.org/packages/release/bioc/html/limma.html
+.. _Galaxy: http://getgalaxy.org
+</help>
+
+</tool>
+
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/differential_count_models/rgedgeRpaired_nocamera.xml	Wed Aug 07 01:58:28 2013 -0400
@@ -0,0 +1,1072 @@
+<tool id="rgDifferentialCount" name="Differential_Count" version="0.20">
+  <description>models using BioConductor packages</description>
+  <requirements>
+      <requirement type="package" version="2.12">biocbasics</requirement>
+      <requirement type="package" version="3.0.1">r3</requirement>
+      <requirement type="package" version="1.3.18">graphicsmagick</requirement>
+      <requirement type="package" version="9.07">ghostscript</requirement>
+  </requirements>
+  
+  <command interpreter="python">
+     rgToolFactory.py --script_path "$runme" --interpreter "Rscript" --tool_name "DifferentialCounts" 
+    --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
+  </command>
+  <inputs>
+    <param name="input1"  type="data" format="tabular" label="Select an input matrix - rows are contigs, columns are counts for each sample"
+       help="Use the HTSeq based count matrix preparation tool to create these matrices from BAM/SAM files and a GTF file of genomic features"/>
+    <param name="title" type="text" value="Differential Counts" size="80" label="Title for job outputs" 
+           help="Supply a meaningful name here to remind you what the outputs contain">
+      <sanitizer invalid_char="">
+        <valid initial="string.letters,string.digits"><add value="_" /> </valid>
+      </sanitizer>
+    </param>
+    <param name="treatment_name" type="text" value="Treatment" size="50" label="Treatment Name"/>
+    <param name="Treat_cols" label="Select columns containing treatment." type="data_column" data_ref="input1" numerical="True" 
+         multiple="true" use_header_names="true" size="120" display="checkboxes">
+        <validator type="no_options" message="Please select at least one column."/>
+    </param>
+    <param name="control_name" type="text" value="Control" size="50" label="Control Name"/>
+    <param name="Control_cols" label="Select columns containing control." type="data_column" data_ref="input1" numerical="True" 
+         multiple="true" use_header_names="true" size="120" display="checkboxes" optional="true">
+    </param>
+    <param name="subjectids" type="text" optional="true" size="120" value = ""
+       label="IF SUBJECTS NOT ALL INDEPENDENT! Enter comma separated strings to indicate sample labels for (eg) pairing - must be one for every column in input"
+       help="Leave blank if no pairing, but eg if data from sample id A99 is in columns 2,4 and id C21 is in 3,5 then enter 'A99,C21,A99,C21'">
+      <sanitizer>
+        <valid initial="string.letters,string.digits"><add value="," /> </valid>
+      </sanitizer>
+    </param>
+    <param name="fQ" type="float" value="0.3" size="5" label="Non-differential contig count quantile threshold - zero to analyze all non-zero read count contigs"
+     help="May be a good or a bad idea depending on the biology and the question. EG 0.3 = sparsest 30% of contigs with at least one read are removed before analysis"/>
+    <param name="useNDF" type="boolean" truevalue="T" falsevalue="F" checked="false" size="1" 
+              label="Non differential filter - remove contigs below a threshold (1 per million) for half or more samples"
+     help="May be a good or a bad idea depending on the biology and the question. This was the old default. Quantile based is available as an alternative"/>
+
+    <conditional name="edgeR">
+        <param name="doedgeR" type="select" 
+           label="Run this model using edgeR"
+           help="edgeR uses a negative binomial model and seems to be powerful, even with few replicates">
+          <option value="F">Do not run edgeR</option>
+          <option value="T" selected="true">Run edgeR</option>
+         </param>
+         <when value="T">
+          <param name="edgeR_priordf" type="integer" value="20" size="3" 
+           label="prior.df for tagwise dispersion - lower value = more emphasis on each tag's variance. Replaces prior.n  and prior.df = prior.n * residual.df"
+           help="0 = Use edgeR default. Use a small value to 'smooth' small samples. See edgeR docs and note below"/>
+         </when>
+         <when value="F"></when>
+    </conditional>
+    <conditional name="DESeq2">
+    <param name="doDESeq2" type="select" 
+       label="Run the same model with DESeq2 and compare findings"
+       help="DESeq2 is an update to the DESeq package. It uses different assumptions and methods to edgeR">
+      <option value="F" selected="true">Do not run DESeq2</option>
+      <option value="T">Run DESeq2</option>
+     </param>
+     <when value="T">
+         <param name="DESeq_fitType" type="select">
+            <option value="parametric" selected="true">Parametric (default) fit for dispersions</option>
+            <option value="local">Local fit - this will automagically be used if parametric fit fails</option>
+            <option value="mean">Mean dispersion fit- use this if you really understand what you're doing - read the fine manual linked below in the documentation</option>
+         </param> 
+     </when>
+     <when value="F"> </when>
+    </conditional>
+    <param name="doVoom" type="select" 
+       label="Run the same model with Voom/limma and compare findings"
+       help="Voom uses counts per million and a precise transformation of variance so count data can be analysed using limma">
+      <option value="F" selected="true">Do not run VOOM</option>
+      <option value="T">Run VOOM</option>
+     </param>
+    <!--
+    <conditional name="camera">
+        <param name="doCamera" type="select" label="Run the edgeR implementation of Camera GSEA for up/down gene sets" 
+            help="If yes, you can choose a set of genesets to test and/or supply a gmt format geneset collection from your history">
+        <option value="F" selected="true">Do not run GSEA tests with the Camera algorithm</option>
+        <option value="T">Run GSEA tests with the Camera algorithm</option>
+        </param>
+         <when value="T">
+         <conditional name="gmtSource">
+          <param name="refgmtSource" type="select" 
+             label="Use a gene set (.gmt) from your history and/or use a built-in (MSigDB etc) gene set">
+            <option value="indexed" selected="true">Use a built-in gene set</option>
+            <option value="history">Use a gene set from my history</option>
+            <option value="both">Add a gene set from my history to a built in gene set</option>
+          </param>
+          <when value="indexed">
+            <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis">
+              <options from_data_table="gseaGMT_3.1">
+                <filter type="sort_by" column="2" />
+                <validator type="no_options" message="No GMT v3.1 files are available - please install them"/>
+              </options>
+            </param>
+          </when>
+          <when value="history">
+            <param name="ownGMT" type="data" format="gmt" label="Select a Gene Set from your history" />
+          </when>
+          <when value="both">
+            <param name="ownGMT" type="data" format="gseagmt" label="Select a Gene Set from your history" />
+            <param name="builtinGMT" type="select" label="Select a gene set matrix (.gmt) file to use for the analysis">
+              <options from_data_table="gseaGMT_4">
+                <filter type="sort_by" column="2" />
+                <validator type="no_options" message="No GMT v4 files are available - please fix tool_data_table and loc files"/>
+              </options>
+            </param>
+           </when>
+         </conditional>
+         </when>
+         <when value="F"> 
+         </when>
+    </conditional>
+    -->
+    <param name="fdrthresh" type="float" value="0.05" size="5" label="P value threshold for FDR filtering for amily wise error rate control"
+     help="Conventional default value of 0.05 recommended"/>
+    <param name="fdrtype" type="select" label="FDR (Type II error) control method" 
+         help="Use fdr or bh typically to control for the number of tests in a reliable way">
+            <option value="fdr" selected="true">fdr</option>
+            <option value="BH">Benjamini Hochberg</option>
+            <option value="BY">Benjamini Yukateli</option>
+            <option value="bonferroni">Bonferroni</option>
+            <option value="hochberg">Hochberg</option>
+            <option value="holm">Holm</option>
+            <option value="hommel">Hommel</option>
+            <option value="none">no control for multiple tests</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out_edgeR" label="${title}_topTable_edgeR.xls">
+         <filter>edgeR['doedgeR'] == "T"</filter>
+    </data>
+    <data format="tabular" name="out_DESeq2" label="${title}_topTable_DESeq2.xls">
+         <filter>DESeq2['doDESeq2'] == "T"</filter>
+    </data>
+    <data format="tabular" name="out_VOOM" label="${title}_topTable_VOOM.xls">
+         <filter>doVoom == "T"</filter>
+    </data>
+    <data format="html" name="html_file" label="${title}.html"/>
+  </outputs>
+ <stdio>
+     <exit_code range="4"   level="fatal"   description="Number of subject ids must match total number of samples in the input matrix" />
+ </stdio>
+ <tests>
+<test>
+<param name='input1' value='test_bams2mx.xls' ftype='tabular' />
+ <param name='treatment_name' value='liver' />
+ <param name='title' value='edgeRtest' />
+ <param name='useNDF' value='' />
+ <param name='doedgeR' value='T' />
+ <param name='doVoom' value='T' />
+ <param name='doDESeq2' value='T' />
+ <param name='fdrtype' value='fdr' />
+ <param name='edgeR_priordf' value="8" />
+ <param name='fdrthresh' value="0.05" />
+ <param name='control_name' value='heart' />
+ <param name='subjectids' value='' />
+ <param name='Control_cols' value='3,4,5,9' />
+ <param name='Treat_cols' value='2,6,7,8' />
+ <output name='out_edgeR' file='edgeRtest1out.xls' compare='diff' />
+ <output name='html_file' file='edgeRtest1out.html'  compare='diff' lines_diff='20' />
+</test>
+</tests>
+
+<configfiles>
+<configfile name="runme">
+<![CDATA[
+# 
+# edgeR.Rscript
+# updated npv 2011 for R 2.14.0 and edgeR 2.4.0 by ross
+# Performs DGE on a count table containing n replicates of two conditions
+#
+# Parameters
+#
+# 1 - Output Dir
+
+# Original edgeR code by: S.Lunke and A.Kaspi
+reallybig = log10(.Machine\$double.xmax)
+reallysmall = log10(.Machine\$double.xmin)
+library('stringr')
+library('gplots')
+library('edgeR')
+hmap2 = function(cmat,nsamp=100,outpdfname='heatmap2.pdf', TName='Treatment',group=NA,myTitle='title goes here')
+{
+# Perform clustering for significant pvalues after controlling FWER
+    samples = colnames(cmat)
+    gu = unique(group)
+    gn = rownames(cmat)
+    if (length(gu) == 2) {
+        col.map = function(g) {if (g==gu[1]) "#FF0000" else "#0000FF"}
+        pcols = unlist(lapply(group,col.map))        
+        } else {
+        colours = rainbow(length(gu),start=0,end=4/6)
+        pcols = colours[match(group,gu)]        }
+    dm = cmat[(! is.na(gn)),] 
+    # remove unlabelled hm rows
+    nprobes = nrow(dm)
+    # sub = paste('Showing',nprobes,'contigs ranked for evidence of differential abundance')
+    if (nprobes > nsamp) {
+      dm =dm[1:nsamp,]
+      #sub = paste('Showing',nsamp,'contigs ranked for evidence for differential abundance out of',nprobes,'total')
+    }
+    newcolnames = substr(colnames(dm),1,20)
+    colnames(dm) = newcolnames
+    pdf(outpdfname)
+    heatmap.2(dm,main=myTitle,ColSideColors=pcols,col=topo.colors(100),dendrogram="col",key=T,density.info='none',
+         Rowv=F,scale='row',trace='none',margins=c(8,8),cexRow=0.4,cexCol=0.5)
+    dev.off()
+}
+
+hmap = function(cmat,nmeans=4,outpdfname="heatMap.pdf",nsamp=250,TName='Treatment',group=NA,myTitle="Title goes here")
+{
+    # for 2 groups only was
+    #col.map = function(g) {if (g==TName) "#FF0000" else "#0000FF"}
+    #pcols = unlist(lapply(group,col.map))
+    gu = unique(group)
+    colours = rainbow(length(gu),start=0.3,end=0.6)
+    pcols = colours[match(group,gu)]
+    nrows = nrow(cmat)
+    mtitle = paste(myTitle,'Heatmap: n contigs =',nrows)
+    if (nrows > nsamp)  {
+               cmat = cmat[c(1:nsamp),]
+               mtitle = paste('Heatmap: Top ',nsamp,' DE contigs (of ',nrows,')',sep='')
+          }
+    newcolnames = substr(colnames(cmat),1,20)
+    colnames(cmat) = newcolnames
+    pdf(outpdfname)
+    heatmap(cmat,scale='row',main=mtitle,cexRow=0.3,cexCol=0.4,Rowv=NA,ColSideColors=pcols)
+    dev.off()
+}
+
+qqPlot = function(descr='qqplot',pvector, outpdf='qqplot.pdf',...)
+# stolen from https://gist.github.com/703512
+{
+    o = -log10(sort(pvector,decreasing=F))
+    e = -log10( 1:length(o)/length(o) )
+    o[o==-Inf] = reallysmall
+    o[o==Inf] = reallybig
+    maint = descr
+    pdf(outpdf)
+    plot(e,o,pch=19,cex=1, main=maint, ...,
+        xlab=expression(Expected~~-log[10](italic(p))),
+        ylab=expression(Observed~~-log[10](italic(p))),
+        xlim=c(0,max(e)), ylim=c(0,max(o)))
+    lines(e,e,col="red")
+    grid(col = "lightgray", lty = "dotted")
+    dev.off()
+}
+
+smearPlot = function(DGEList,deTags, outSmear, outMain)
+        {
+        pdf(outSmear)
+        plotSmear(DGEList,de.tags=deTags,main=outMain)
+        grid(col="lightgray", lty="dotted")
+        dev.off()
+        }
+        
+boxPlot = function(rawrs,cleanrs,maint,myTitle,pdfname)
+{   # 
+        nc = ncol(rawrs)
+        for (i in c(1:nc)) {rawrs[(rawrs[,i] < 0),i] = NA}
+        fullnames = colnames(rawrs)
+        newcolnames = substr(colnames(rawrs),1,20)
+        colnames(rawrs) = newcolnames
+        newcolnames = substr(colnames(cleanrs),1,20)
+        colnames(cleanrs) = newcolnames
+        defpar = par(no.readonly=T)
+        print.noquote('raw contig counts by sample:')
+        print.noquote(summary(rawrs))
+        print.noquote('normalised contig counts by sample:')
+        print.noquote(summary(cleanrs))
+        pdf(pdfname)
+        par(mfrow=c(1,2))
+        boxplot(rawrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('Raw:',maint))
+        grid(col="lightgray",lty="dotted")
+        boxplot(cleanrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('After ',maint))
+        grid(col="lightgray",lty="dotted")
+        dev.off()
+        pdfname = "sample_counts_histogram.pdf" 
+        nc = ncol(rawrs)
+        print.noquote(paste('Using ncol rawrs=',nc))
+        ncroot = round(sqrt(nc))
+        if (ncroot*ncroot < nc) { ncroot = ncroot + 1 }
+        m = c()
+        for (i in c(1:nc)) {
+              rhist = hist(rawrs[,i],breaks=100,plot=F)
+              m = append(m,max(rhist\$counts))
+             }
+        ymax = max(m)
+        ncols = length(fullnames)
+        if (ncols > 20) 
+        {
+           scale = 7*ncols/20
+           pdf(pdfname,width=scale,height=scale)
+        } else { 
+           pdf(pdfname)
+        }
+        par(mfrow=c(ncroot,ncroot))
+        for (i in c(1:nc)) {
+                 hist(rawrs[,i], main=paste("Contig logcount",i), xlab='log raw count', col="maroon", 
+                 breaks=100,sub=fullnames[i],cex=0.8,ylim=c(0,ymax))
+             }
+        dev.off()
+        par(defpar)
+      
+}
+
+cumPlot = function(rawrs,cleanrs,maint,myTitle)
+{   # updated to use ecdf
+        pdfname = "Filtering_rowsum_bar_charts.pdf"
+        defpar = par(no.readonly=T)
+        lrs = log(rawrs,10) 
+        lim = max(lrs)
+        pdf(pdfname)
+        par(mfrow=c(2,1))
+        hist(lrs,breaks=100,main=paste('Before:',maint),xlab="# Reads (log)",
+             ylab="Count",col="maroon",sub=myTitle, xlim=c(0,lim),las=1)
+        grid(col="lightgray", lty="dotted")
+        lrs = log(cleanrs,10) 
+        hist(lrs,breaks=100,main=paste('After:',maint),xlab="# Reads (log)",
+             ylab="Count",col="maroon",sub=myTitle,xlim=c(0,lim),las=1)
+        grid(col="lightgray", lty="dotted")
+        dev.off()
+        par(defpar)
+}
+
+cumPlot1 = function(rawrs,cleanrs,maint,myTitle)
+{   # updated to use ecdf
+        pdfname = paste(gsub(" ","", myTitle , fixed=TRUE),"RowsumCum.pdf",sep='_')
+        pdf(pdfname)
+        par(mfrow=c(2,1))
+        lastx = max(rawrs)
+        rawe = knots(ecdf(rawrs))
+        cleane = knots(ecdf(cleanrs))
+        cy = 1:length(cleane)/length(cleane)
+        ry = 1:length(rawe)/length(rawe)
+        plot(rawe,ry,type='l',main=paste('Before',maint),xlab="Log Contig Total Reads",
+             ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle)
+        grid(col="blue")
+        plot(cleane,cy,type='l',main=paste('After',maint),xlab="Log Contig Total Reads",
+             ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle)
+        grid(col="blue")
+        dev.off()
+}
+
+
+
+doGSEAold = function(y=NULL,design=NULL,histgmt="",
+                  bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
+                  ntest=0, myTitle="myTitle", outfname="GSEA.xls", minnin=5, maxnin=2000,fdrthresh=0.05,fdrtype="BH")
+{
+  sink('Camera.log')
+  genesets = c()
+  if (bigmt > "")
+  {
+    bigenesets = readLines(bigmt)
+    genesets = bigenesets
+  }
+  if (histgmt > "")
+  {
+    hgenesets = readLines(histgmt)
+    if (bigmt > "") {
+      genesets = rbind(genesets,hgenesets)
+    } else {
+      genesets = hgenesets
+    } # use only history if no bi
+  }
+  print.noquote(paste("@@@read",length(genesets), 'genesets from',histgmt,bigmt))
+  genesets = strsplit(genesets,'\t') # tabular. genesetid\tURLorwhatever\tgene_1\t..\tgene_n
+  outf = outfname
+  head=paste(myTitle,'edgeR GSEA')
+  write(head,file=outfname,append=F)
+  ntest=length(genesets)
+  urownames = toupper(rownames(y))
+  upcam = c()
+  downcam = c()
+  for (i in 1:ntest) {
+    gs = unlist(genesets[i])
+    g = gs[1] # geneset_id
+    u = gs[2]
+    if (u > "") { u = paste("<a href=\'",u,"\'>",u,"</a>",sep="") }
+    glist = gs[3:length(gs)] # member gene symbols
+    glist = toupper(glist)
+    inglist = urownames %in% glist
+    nin = sum(inglist)
+    if ((nin > minnin) && (nin < maxnin)) {
+      ### print(paste('@@found',sum(inglist),'genes in glist'))
+      camres = camera(y=y,index=inglist,design=design)
+      if (! is.null(camres)) {
+      rownames(camres) = g # gene set name
+      camres = cbind(GeneSet=g,URL=u,camres)
+      if (camres\$Direction == "Up") 
+        {
+        upcam = rbind(upcam,camres) } else {
+          downcam = rbind(downcam,camres)
+        }
+      }
+   }
+  }
+  uscam = upcam[order(upcam\$PValue),]
+  unadjp = uscam\$PValue
+  uscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
+  nup = max(10,sum((uscam\$adjPValue < fdrthresh)))
+  dscam = downcam[order(downcam\$PValue),]
+  unadjp = dscam\$PValue
+  dscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
+  ndown = max(10,sum((dscam\$adjPValue < fdrthresh)))
+  write.table(uscam,file=paste('camera_up',outfname,sep='_'),quote=F,sep='\t',row.names=F)
+  write.table(dscam,file=paste('camera_down',outfname,sep='_'),quote=F,sep='\t',row.names=F)
+  print.noquote(paste('@@@@@ Camera up top',nup,'gene sets:'))
+  write.table(head(uscam,nup),file="",quote=F,sep='\t',row.names=F)
+  print.noquote(paste('@@@@@ Camera down top',ndown,'gene sets:'))
+  write.table(head(dscam,ndown),file="",quote=F,sep='\t',row.names=F)
+  sink()
+}
+
+
+
+
+doGSEA = function(y=NULL,design=NULL,histgmt="",
+                  bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
+                  ntest=0, myTitle="myTitle", outfname="GSEA.xls", minnin=5, maxnin=2000,fdrthresh=0.05,fdrtype="BH")
+{
+  sink('Camera.log')
+  genesets = c()
+  if (bigmt > "")
+  {
+    bigenesets = readLines(bigmt)
+    genesets = bigenesets
+  }
+  if (histgmt > "")
+  {
+    hgenesets = readLines(histgmt)
+    if (bigmt > "") {
+      genesets = rbind(genesets,hgenesets)
+    } else {
+      genesets = hgenesets
+    } # use only history if no bi
+  }
+  print.noquote(paste("@@@read",length(genesets), 'genesets from',histgmt,bigmt))
+  genesets = strsplit(genesets,'\t') # tabular. genesetid\tURLorwhatever\tgene_1\t..\tgene_n
+  outf = outfname
+  head=paste(myTitle,'edgeR GSEA')
+  write(head,file=outfname,append=F)
+  ntest=length(genesets)
+  urownames = toupper(rownames(y))
+  upcam = c()
+  downcam = c()
+  incam = c()
+  urls = c()
+  gsids = c()
+  for (i in 1:ntest) {
+    gs = unlist(genesets[i])
+    gsid = gs[1] # geneset_id
+    url = gs[2]
+    if (url > "") { url = paste("<a href=\'",url,"\'>",url,"</a>",sep="") }
+    glist = gs[3:length(gs)] # member gene symbols
+    glist = toupper(glist)
+    inglist = urownames %in% glist
+    nin = sum(inglist)
+    if ((nin > minnin) && (nin < maxnin)) {
+      incam = c(incam,inglist)
+      gsids = c(gsids,gsid)
+      urls = c(urls,url)
+    }
+  }
+  incam = as.list(incam)
+  names(incam) = gsids
+  allcam = camera(y=y,index=incam,design=design)
+  allcamres = cbind(geneset=gsids,allcam,URL=urls)
+  for (i in 1:ntest) {
+    camres = allcamres[i]
+    res = try(test = (camres\$Direction == "Up"))
+    if ("try-error" %in% class(res)) {
+      cat("test failed, camres = :")
+      print.noquote(camres)
+    } else  { if (camres\$Direction == "Up")
+    {  upcam = rbind(upcam,camres)
+    } else { downcam = rbind(downcam,camres)
+    }
+              
+    }
+  }
+  uscam = upcam[order(upcam\$PValue),]
+  unadjp = uscam\$PValue
+  uscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
+  nup = max(10,sum((uscam\$adjPValue < fdrthresh)))
+  dscam = downcam[order(downcam\$PValue),]
+  unadjp = dscam\$PValue
+  dscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
+  ndown = max(10,sum((dscam\$adjPValue < fdrthresh)))
+  write.table(uscam,file=paste('camera_up',outfname,sep='_'),quote=F,sep='\t',row.names=F)
+  write.table(dscam,file=paste('camera_down',outfname,sep='_'),quote=F,sep='\t',row.names=F)
+  print.noquote(paste('@@@@@ Camera up top',nup,'gene sets:'))
+  write.table(head(uscam,nup),file="",quote=F,sep='\t',row.names=F)
+  print.noquote(paste('@@@@@ Camera down top',ndown,'gene sets:'))
+  write.table(head(dscam,ndown),file="",quote=F,sep='\t',row.names=F)
+  sink()
+  }
+ 
+
+edgeIt = function (Count_Matrix=c(),group=c(),out_edgeR=F,out_VOOM=F,out_DESeq2=F,fdrtype='fdr',priordf=5, 
+        fdrthresh=0.05,outputdir='.', myTitle='Differential Counts',libSize=c(),useNDF=F,
+        filterquantile=0.2, subjects=c(),mydesign=NULL,
+        doDESeq2=T,doVoom=T,doCamera=T,doedgeR=T,org='hg19',
+        histgmt="", bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
+        doCook=F,DESeq_fitType="parameteric") 
+{
+  # Error handling
+  if (length(unique(group))!=2){
+    print("Number of conditions identified in experiment does not equal 2")
+    q()
+    }
+  require(edgeR)
+  options(width = 512) 
+  mt = paste(unlist(strsplit(myTitle,'_')),collapse=" ")
+  allN = nrow(Count_Matrix)
+  nscut = round(ncol(Count_Matrix)/2)
+  colTotmillionreads = colSums(Count_Matrix)/1e6
+  counts.dataframe = as.data.frame(c()) 
+  rawrs = rowSums(Count_Matrix)
+  nonzerod = Count_Matrix[(rawrs > 0),] # remove all zero count genes
+  nzN = nrow(nonzerod)
+  nzrs = rowSums(nonzerod)
+  zN = allN - nzN
+  print('# Quantiles for non-zero row counts:',quote=F)
+  print(quantile(nzrs,probs=seq(0,1,0.1)),quote=F)
+  if (useNDF == T)
+  {
+    gt1rpin3 = rowSums(Count_Matrix/expandAsMatrix(colTotmillionreads,dim(Count_Matrix)) >= 1) >= nscut
+    lo = colSums(Count_Matrix[!gt1rpin3,])
+    workCM = Count_Matrix[gt1rpin3,]
+    cleanrs = rowSums(workCM)
+    cleanN = length(cleanrs)
+    meth = paste( "After removing",length(lo),"contigs with fewer than ",nscut," sample read counts >= 1 per million, there are",sep="")
+    print(paste("Read",allN,"contigs. Removed",zN,"contigs with no reads.",meth,cleanN,"contigs"),quote=F)
+    maint = paste('Filter >=1/million reads in >=',nscut,'samples')
+  }   else {        
+    useme = (nzrs > quantile(nzrs,filterquantile))
+    workCM = nonzerod[useme,]
+    lo = colSums(nonzerod[!useme,])
+    cleanrs = rowSums(workCM)
+    cleanN = length(cleanrs)
+    meth = paste("After filtering at count quantile =",filterquantile,", there are",sep="")
+    print(paste('Read',allN,"contigs. Removed",zN,"with no reads.",meth,cleanN,"contigs"),quote=F)
+    maint = paste('Filter below',filterquantile,'quantile')
+  }
+  cumPlot(rawrs=rawrs,cleanrs=cleanrs,maint=maint,myTitle=myTitle)
+  allgenes = rownames(workCM)
+  reg = "^chr([0-9]+):([0-9]+)-([0-9]+)"
+  genecards="<a href=\'http://www.genecards.org/index.php?path=/Search/keyword/"
+  ucsc = paste("<a href=\'http://genome.ucsc.edu/cgi-bin/hgTracks?db=",org,sep='')
+  testreg = str_match(allgenes,reg)
+  if (sum(!is.na(testreg[,1]))/length(testreg[,1]) > 0.8) # is ucsc style string
+  {
+    print("@@ using ucsc substitution for urls")
+    contigurls = paste0(ucsc,"&amp;position=chr",testreg[,2],":",testreg[,3],"-",testreg[,4],"\'>",allgenes,"</a>")
+  } else {
+    print("@@ using genecards substitution for urls")
+    contigurls = paste0(genecards,allgenes,"\'>",allgenes,"</a>")
+  }
+  print.noquote("# urls")
+  print.noquote(head(contigurls))
+  print(paste("# Total low count contigs per sample = ",paste(lo,collapse=',')),quote=F) 
+  cmrowsums = rowSums(workCM)
+  TName=unique(group)[1]
+  CName=unique(group)[2]
+  if (is.null(mydesign)) {
+    if (length(subjects) == 0) 
+    {
+      mydesign = model.matrix(~group)
+    } 
+    else { 
+      subjf = factor(subjects)
+      mydesign = model.matrix(~subjf+group) # we block on subject so make group last to simplify finding it
+    }
+  } 
+  print.noquote(paste('Using samples:',paste(colnames(workCM),collapse=',')))
+  print.noquote('Using design matrix:')
+  print.noquote(mydesign)
+  if (doedgeR) {
+  sink('edgeR.log')
+  #### Setup DGEList object
+  DGEList = DGEList(counts=workCM, group = group)
+  DGEList = calcNormFactors(DGEList)
+
+  DGEList = estimateGLMCommonDisp(DGEList,mydesign)
+  comdisp = DGEList\$common.dispersion
+  DGEList = estimateGLMTrendedDisp(DGEList,mydesign)
+  if (edgeR_priordf > 0) {
+    print.noquote(paste("prior.df =",edgeR_priordf))
+    DGEList = estimateGLMTagwiseDisp(DGEList,mydesign,prior.df = edgeR_priordf)
+  } else {
+    DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
+  }
+  DGLM = glmFit(DGEList,design=mydesign)
+  DE = glmLRT(DGLM,coef=ncol(DGLM\$design)) # always last one - subject is first if needed
+  efflib = DGEList\$samples\$lib.size*DGEList\$samples\$norm.factors
+  normData = (1e+06*DGEList\$counts/efflib)
+  uoutput = cbind( 
+    Name=as.character(rownames(DGEList\$counts)),
+    DE\$table,
+    adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
+    Dispersion=DGEList\$tagwise.dispersion,totreads=cmrowsums,normData,
+    DGEList\$counts
+  )
+  soutput = uoutput[order(DE\$table\$PValue),] # sorted into p value order - for quick toptable
+  goodness = gof(DGLM, pcutoff=fdrthresh)
+  if (sum(goodness\$outlier) > 0) {
+    print.noquote('GLM outliers:')
+    print(paste(rownames(DGLM)[(goodness\$outlier)],collapse=','),quote=F)
+    } else { 
+      print('No GLM fit outlier genes found\n')
+    }
+  z = limma::zscoreGamma(goodness\$gof.statistic, shape=goodness\$df/2, scale=2)
+  pdf("edgeR_GoodnessofFit.pdf")
+  qq = qqnorm(z, panel.first=grid(), main="tagwise dispersion")
+  abline(0,1,lwd=3)
+  points(qq\$x[goodness\$outlier],qq\$y[goodness\$outlier], pch=16, col="maroon")
+  dev.off()
+  estpriorn = getPriorN(DGEList)
+  print(paste("Common Dispersion =",comdisp,"CV = ",sqrt(comdisp),"getPriorN = ",estpriorn),quote=F)
+  efflib = DGEList\$samples\$lib.size*DGEList\$samples\$norm.factors
+  normData = (1e+06*DGEList\$counts/efflib)
+  uniqueg = unique(group)
+  #### Plot MDS
+  sample_colors =  match(group,levels(group))
+  sampleTypes = levels(factor(group))
+  print.noquote(sampleTypes)
+  pdf("edgeR_MDSplot.pdf")
+  plotMDS.DGEList(DGEList,main=paste("edgeR MDS for",myTitle),cex=0.5,col=sample_colors,pch=sample_colors)
+  legend(x="topleft", legend = sampleTypes,col=c(1:length(sampleTypes)), pch=19)
+  grid(col="blue")
+  dev.off()
+  colnames(normData) = paste( colnames(normData),'N',sep="_")
+  print(paste('Raw sample read totals',paste(colSums(nonzerod,na.rm=T),collapse=',')))
+  nzd = data.frame(log(nonzerod + 1e-2,10))
+  try( boxPlot(rawrs=nzd,cleanrs=log(normData,10),maint='TMM Normalisation',myTitle=myTitle,pdfname="edgeR_raw_norm_counts_box.pdf") )
+  write.table(soutput,file=out_edgeR, quote=FALSE, sep="\t",row.names=F)
+  tt = cbind( 
+    Name=as.character(rownames(DGEList\$counts)),
+    DE\$table,
+    adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
+    Dispersion=DGEList\$tagwise.dispersion,totreads=cmrowsums
+  )
+  print.noquote("# edgeR Top tags\n")
+  tt = cbind(tt,URL=contigurls) # add to end so table isn't laid out strangely
+  tt = tt[order(DE\$table\$PValue),] 
+  print.noquote(tt[1:50,])
+  deTags = rownames(uoutput[uoutput\$adj.p.value < fdrthresh,])
+  nsig = length(deTags)
+  print(paste('#',nsig,'tags significant at adj p=',fdrthresh),quote=F)
+  deColours = ifelse(deTags,'red','black')
+  pdf("edgeR_BCV_vs_abundance.pdf")
+  plotBCV(DGEList, cex=0.3, main="Biological CV vs abundance")
+  dev.off()
+  dg = DGEList[order(DE\$table\$PValue),]
+  #normData = (1e+06 * dg\$counts/expandAsMatrix(dg\$samples\$lib.size, dim(dg)))
+  efflib = dg\$samples\$lib.size*dg\$samples\$norm.factors
+  normData = (1e+06*dg\$counts/efflib)
+  outpdfname="edgeR_top_100_heatmap.pdf"
+  hmap2(normData,nsamp=100,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste('edgeR Heatmap',myTitle))
+  outSmear = "edgeR_smearplot.pdf"
+  outMain = paste("Smear Plot for ",TName,' Vs ',CName,' (FDR@',fdrthresh,' N = ',nsig,')',sep='')
+  smearPlot(DGEList=DGEList,deTags=deTags, outSmear=outSmear, outMain = outMain)
+  qqPlot(descr=paste(myTitle,'edgeR adj p QQ plot'),pvector=tt\$adj.p.value,outpdf='edgeR_qqplot.pdf')
+  norm.factor = DGEList\$samples\$norm.factors
+  topresults.edgeR = soutput[which(soutput\$adj.p.value < fdrthresh), ]
+  edgeRcountsindex = which(allgenes %in% rownames(topresults.edgeR))
+  edgeRcounts = rep(0, length(allgenes))
+  edgeRcounts[edgeRcountsindex] = 1  # Create venn diagram of hits
+  sink()
+  } ### doedgeR
+  if (doDESeq2 == T)
+  {
+    sink("DESeq2.log")
+    # DESeq2
+    require('DESeq2')
+    library('RColorBrewer')
+    if (length(subjects) == 0)
+        {
+        pdata = data.frame(Name=colnames(workCM),Rx=group,row.names=colnames(workCM))
+        deSEQds = DESeqDataSetFromMatrix(countData = workCM,  colData = pdata, design = formula(~ Rx))
+        } else {
+        pdata = data.frame(Name=colnames(workCM),Rx=group,subjects=subjects,row.names=colnames(workCM))
+        deSEQds = DESeqDataSetFromMatrix(countData = workCM,  colData = pdata, design = formula(~ subjects + Rx))
+        }
+    #DESeq2 = DESeq(deSEQds,fitType='local',pAdjustMethod=fdrtype)
+    #rDESeq = results(DESeq2)
+    #newCountDataSet(workCM, group)
+    deSeqDatsizefac = estimateSizeFactors(deSEQds)
+    deSeqDatdisp = estimateDispersions(deSeqDatsizefac,fitType=DESeq_fitType)
+    resDESeq = nbinomWaldTest(deSeqDatdisp, pAdjustMethod=fdrtype)
+    rDESeq = as.data.frame(results(resDESeq))
+    rDESeq = cbind(Contig=rownames(workCM),rDESeq,NReads=cmrowsums,URL=contigurls)
+    srDESeq = rDESeq[order(rDESeq\$pvalue),]
+    qqPlot(descr=paste(myTitle,'DESeq2 adj p qq plot'),pvector=rDESeq\$padj,outpdf='DESeq2_qqplot.pdf')
+    cat("# DESeq top 50\n")
+    print.noquote(srDESeq[1:50,])
+    write.table(srDESeq,file=out_DESeq2, quote=FALSE, sep="\t",row.names=F)
+    topresults.DESeq = rDESeq[which(rDESeq\$padj < fdrthresh), ]
+    DESeqcountsindex = which(allgenes %in% rownames(topresults.DESeq))
+    DESeqcounts = rep(0, length(allgenes))
+    DESeqcounts[DESeqcountsindex] = 1
+    pdf("DESeq2_dispersion_estimates.pdf")
+    plotDispEsts(resDESeq)
+    dev.off()
+    ysmall = abs(min(rDESeq\$log2FoldChange))
+    ybig = abs(max(rDESeq\$log2FoldChange))
+    ylimit = min(4,ysmall,ybig)
+    pdf("DESeq2_MA_plot.pdf")
+    plotMA(resDESeq,main=paste(myTitle,"DESeq2 MA plot"),ylim=c(-ylimit,ylimit))
+    dev.off()
+    rlogres = rlogTransformation(resDESeq)
+    sampledists = dist( t( assay(rlogres) ) )
+    sdmat = as.matrix(sampledists)
+    pdf("DESeq2_sample_distance_plot.pdf")
+    heatmap.2(sdmat,trace="none",main=paste(myTitle,"DESeq2 sample distances"),
+         col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255))
+    dev.off()
+    ###outpdfname="DESeq2_top50_heatmap.pdf"
+    ###hmap2(sresDESeq,nsamp=50,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste('DESeq2 vst rlog Heatmap',myTitle))
+    sink()
+    result = try( (ppca = plotPCA( varianceStabilizingTransformation(deSeqDatdisp,blind=T), intgroup=c("Rx","Name")) ) )
+    if ("try-error" %in% class(result)) {
+         print.noquote('DESeq2 plotPCA failed.')
+         } else {
+         pdf("DESeq2_PCA_plot.pdf")
+         #### wtf - print? Seems needed to get this to work
+         print(ppca)
+         dev.off()
+        }
+  }
+
+  if (doVoom == T) {
+      sink('VOOM.log')
+      if (doedgeR == F) {
+         #### Setup DGEList object
+         DGEList = DGEList(counts=workCM, group = group)
+         DGEList = calcNormFactors(DGEList)
+         DGEList = estimateGLMCommonDisp(DGEList,mydesign)
+         DGEList = estimateGLMTrendedDisp(DGEList,mydesign)
+         DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
+         DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
+         norm.factor = DGEList\$samples\$norm.factors
+         }
+      pdf("VOOM_mean_variance_plot.pdf")
+      dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = colSums(workCM) * norm.factor)
+      dev.off()
+      # Use limma to fit data
+      fit = lmFit(dat.voomed, mydesign)
+      fit = eBayes(fit)
+      rvoom = topTable(fit, coef = length(colnames(mydesign)), adj = fdrtype, n = Inf, sort="none")
+      qqPlot(descr=paste(myTitle,'VOOM-limma adj p QQ plot'),pvector=rvoom\$adj.P.Val,outpdf='VOOM_qqplot.pdf')
+      rownames(rvoom) = rownames(workCM)
+      rvoom = cbind(rvoom,NReads=cmrowsums,URL=contigurls)
+      srvoom = rvoom[order(rvoom\$P.Value),]
+      cat("# VOOM top 50\n")
+      print(srvoom[1:50,])
+      write.table(srvoom,file=out_VOOM, quote=FALSE, sep="\t",row.names=F)
+      # Use an FDR cutoff to find interesting samples for edgeR, DESeq and voom/limma
+      topresults.voom = rvoom[which(rvoom\$adj.P.Val < fdrthresh), ]
+      voomcountsindex = which(allgenes %in% topresults.voom\$ID)
+      voomcounts = rep(0, length(allgenes))
+      voomcounts[voomcountsindex] = 1
+      sink()
+  }
+
+  if (doCamera) {
+  doGSEA(y=DGEList,design=mydesign,histgmt=histgmt,bigmt=bigmt,ntest=20,myTitle=myTitle,
+    outfname=paste(mt,"GSEA.xls",sep="_"),fdrthresh=fdrthresh,fdrtype=fdrtype)
+  }
+
+  if ((doDESeq2==T) || (doVoom==T) || (doedgeR==T)) {
+    if ((doVoom==T) && (doDESeq2==T) && (doedgeR==T)) {
+        vennmain = paste(mt,'Voom,edgeR and DESeq2 overlap at FDR=',fdrthresh)
+        counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts, 
+                                       VOOM_limma = voomcounts, row.names = allgenes)
+       } else if ((doDESeq2==T) && (doedgeR==T))  {
+         vennmain = paste(mt,'DESeq2 and edgeR overlap at FDR=',fdrthresh)
+         counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts, row.names = allgenes)
+       } else if ((doVoom==T) && (doedgeR==T)) {
+        vennmain = paste(mt,'Voom and edgeR overlap at FDR=',fdrthresh)
+        counts.dataframe = data.frame(edgeR = edgeRcounts, VOOM_limma = voomcounts, row.names = allgenes)
+       }
+    
+    if (nrow(counts.dataframe > 1)) {
+      counts.venn = vennCounts(counts.dataframe)
+      vennf = "Venn_significant_genes_overlap.pdf" 
+      pdf(vennf)
+      vennDiagram(counts.venn,main=vennmain,col="maroon")
+      dev.off()
+    }
+  } #### doDESeq2 or doVoom
+  
+}
+#### Done
+
+###sink(stdout(),append=T,type="message")
+builtin_gmt = ""
+history_gmt = ""
+history_gmt_name = ""
+out_edgeR = F
+out_DESeq2 = F
+out_VOOM = "$out_VOOM"
+doDESeq2 = $DESeq2.doDESeq2 # make these T or F
+doVoom = $doVoom
+doCamera = F
+doedgeR = $edgeR.doedgeR
+edgeR_priordf = 0
+
+
+#if $doVoom == "T":
+  out_VOOM = "$out_VOOM"
+#end if
+
+#if $DESeq2.doDESeq2 == "T":
+  out_DESeq2 = "$out_DESeq2"
+  DESeq_fitType = "$DESeq2.DESeq_fitType"
+#end if
+
+#if $edgeR.doedgeR == "T":
+  out_edgeR = "$out_edgeR"
+  edgeR_priordf = $edgeR.edgeR_priordf  
+#end if
+
+
+if (sum(c(doedgeR,doVoom,doDESeq2)) == 0)
+{
+write("No methods chosen - nothing to do! Please try again after choosing one or more methods", stderr())
+quit(save="no",status=2)
+}
+
+Out_Dir = "$html_file.files_path"
+Input =  "$input1"
+TreatmentName = "$treatment_name"
+TreatmentCols = "$Treat_cols"
+ControlName = "$control_name"
+ControlCols= "$Control_cols"
+org = "$input1.dbkey"
+if (org == "") { org = "hg19"}
+fdrtype = "$fdrtype"
+fdrthresh = $fdrthresh
+useNDF = $useNDF
+fQ = $fQ # non-differential centile cutoff
+myTitle = "$title"
+sids = strsplit("$subjectids",',')
+subjects = unlist(sids)
+nsubj = length(subjects)
+TCols = as.numeric(strsplit(TreatmentCols,",")[[1]])-1
+CCols = as.numeric(strsplit(ControlCols,",")[[1]])-1 
+cat('Got TCols=')
+cat(TCols)
+cat('; CCols=')
+cat(CCols)
+cat('\n')
+useCols = c(TCols,CCols)
+if (file.exists(Out_Dir) == F) dir.create(Out_Dir)
+Count_Matrix = read.table(Input,header=T,row.names=1,sep='\t') #Load tab file assume header
+snames = colnames(Count_Matrix)
+nsamples = length(snames)
+if (nsubj >  0 & nsubj != nsamples) {
+options("show.error.messages"=T)
+mess = paste('Fatal error: Supplied subject id list',paste(subjects,collapse=','),
+   'has length',nsubj,'but there are',nsamples,'samples',paste(snames,collapse=','))
+write(mess, stderr())
+quit(save="no",status=4)
+}
+if (length(subjects) != 0) {subjects = subjects[useCols]}
+Count_Matrix = Count_Matrix[,useCols] ### reorder columns
+rn = rownames(Count_Matrix)
+islib = rn %in% c('librarySize','NotInBedRegions')
+LibSizes = Count_Matrix[subset(rn,islib),][1] # take first
+Count_Matrix = Count_Matrix[subset(rn,! islib),]
+group = c(rep(TreatmentName,length(TCols)), rep(ControlName,length(CCols)) )             #Build a group descriptor
+group = factor(group, levels=c(ControlName,TreatmentName))
+colnames(Count_Matrix) = paste(group,colnames(Count_Matrix),sep="_")                   #Relable columns
+results = edgeIt(Count_Matrix=Count_Matrix,group=group, out_edgeR=out_edgeR, out_VOOM=out_VOOM, out_DESeq2=out_DESeq2,
+                 fdrtype='BH',mydesign=NULL,priordf=edgeR_priordf,fdrthresh=fdrthresh,outputdir='.',
+                 myTitle=myTitle,useNDF=F,libSize=c(),filterquantile=fQ,subjects=subjects,
+                 doDESeq2=doDESeq2,doVoom=doVoom,doCamera=doCamera,doedgeR=doedgeR,org=org,
+                 histgmt=history_gmt,bigmt=builtin_gmt,DESeq_fitType=DESeq_fitType)
+sessionInfo()
+]]>
+</configfile>
+</configfiles>
+<help>
+
+**What it does**
+
+Allows short read sequence counts from controlled experiments to be analysed for differentially expressed genes.
+Optionally adds a term for subject if not all samples are independent or if some other factor needs to be blocked in the design.
+
+**Input**
+
+Requires a count matrix as a tabular file. These are best made using the companion HTSeq_ based counter Galaxy wrapper
+and your fave gene model to generate inputs. Each row is a genomic feature (gene or exon eg) and each column the 
+non-negative integer count of reads from one sample overlapping the feature. 
+The matrix must have a header row uniquely identifying the source samples, and unique row names in 
+the first column. Typically the row names are gene symbols or probe ids for downstream use in GSEA and other methods.
+
+**Specifying comparisons**
+
+This is basically dumbed down for two factors - case vs control.
+
+More complex interfaces are possible but painful at present. 
+Probably need to specify a phenotype file to do this better.
+Work in progress. Send code.
+
+If you have (eg) paired samples and wish to include a term in the GLM to account for some other factor (subject in the case of paired samples),
+put a comma separated list of indicators for every sample (whether modelled or not!) indicating (eg) the subject number or 
+A list of integers, one for each subject or an empty string if samples are all independent.
+If not empty, there must be exactly as many integers in the supplied integer list as there are columns (samples) in the count matrix.
+Integers for samples that are not in the analysis *must* be present in the string as filler even if not used.
+
+So if you have 2 pairs out of 6 samples, you need to put in unique integers for the unpaired ones
+eg if you had 6 samples with the first two independent but the second and third pairs each being from independent subjects. you might use
+8,9,1,1,2,2 
+as subject IDs to indicate two paired samples from the same subject in columns 3/4 and 5/6
+
+**Methods available**
+
+You can run 3 popular Bioconductor packages available for count data.
+
+edgeR - see edgeR_ for details
+
+VOOM/limma - see limma_VOOM_ for details
+
+DESeq2 - see DESeq2_ for details
+
+and optionally camera in edgeR which works better if MSigDB is installed.
+
+**Outputs**
+
+Some helpful plots and analysis results. Note that most of these are produced using R code 
+suggested by the excellent documentation and vignettes for the Bioconductor
+packages invoked. The Tool Factory is used to automatically lay these out for you to enjoy.
+
+**Note on Voom**
+
+The voom from limma version 3.16.6 help in R includes this from the authors - but you should read the paper to interpret this method.
+
+This function is intended to process RNA-Seq or ChIP-Seq data prior to linear modelling in limma.
+
+voom is an acronym for mean-variance modelling at the observational level.
+The key concern is to estimate the mean-variance relationship in the data, then use this to compute appropriate weights for each observation.
+Count data almost show non-trivial mean-variance relationships. Raw counts show increasing variance with increasing count size, while log-counts typically show a decreasing mean-variance trend.
+This function estimates the mean-variance trend for log-counts, then assigns a weight to each observation based on its predicted variance.
+The weights are then used in the linear modelling process to adjust for heteroscedasticity.
+
+In an experiment, a count value is observed for each tag in each sample. A tag-wise mean-variance trend is computed using lowess.
+The tag-wise mean is the mean log2 count with an offset of 0.5, across samples for a given tag.
+The tag-wise variance is the quarter-root-variance of normalized log2 counts per million values with an offset of 0.5, across samples for a given tag.
+Tags with zero counts across all samples are not included in the lowess fit. Optional normalization is performed using normalizeBetweenArrays.
+Using fitted values of log2 counts from a linear model fit by lmFit, variances from the mean-variance trend were interpolated for each observation.
+This was carried out by approxfun. Inverse variance weights can be used to correct for mean-variance trend in the count data.
+
+
+Author(s)
+
+Charity Law and Gordon Smyth
+
+References
+
+Law, CW (2013). Precision weights for gene expression analysis. PhD Thesis. University of Melbourne, Australia.
+
+Law, CW, Chen, Y, Shi, W, Smyth, GK (2013). Voom! Precision weights unlock linear model analysis tools for RNA-seq read counts.
+Technical Report 1 May 2013, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Reseach, Melbourne, Australia.
+http://www.statsci.org/smyth/pubs/VoomPreprint.pdf
+
+See Also
+
+A voom case study is given in the edgeR User's Guide.
+
+vooma is a similar function but for microarrays instead of RNA-seq.
+
+
+***old rant on changes to Bioconductor package variable names between versions***
+
+The edgeR authors made a small cosmetic change in the name of one important variable (from p.value to PValue) 
+breaking this and all other code that assumed the old name for this variable, 
+between edgeR2.4.4 and 2.4.6 (the version for R 2.14 as at the time of writing). 
+This means that all code using edgeR is sensitive to the version. I think this was a very unwise thing 
+to do because it wasted hours of my time to track down and will similarly cost other edgeR users dearly
+when their old scripts break. This tool currently now works with 2.4.6.
+
+**Note on prior.N**
+
+http://seqanswers.com/forums/showthread.php?t=5591 says:
+
+*prior.n*
+
+The value for prior.n determines the amount of smoothing of tagwise dispersions towards the common dispersion. 
+You can think of it as like a "weight" for the common value. (It is actually the weight for the common likelihood 
+in the weighted likelihood equation). The larger the value for prior.n, the more smoothing, i.e. the closer your 
+tagwise dispersion estimates will be to the common dispersion. If you use a prior.n of 1, then that gives the 
+common likelihood the weight of one observation.
+
+In answer to your question, it is a good thing to squeeze the tagwise dispersions towards a common value, 
+or else you will be using very unreliable estimates of the dispersion. I would not recommend using the value that 
+you obtained from estimateSmoothing()---this is far too small and would result in virtually no moderation 
+(squeezing) of the tagwise dispersions. How many samples do you have in your experiment? 
+What is the experimental design? If you have few samples (less than 6) then I would suggest a prior.n of at least 10. 
+If you have more samples, then the tagwise dispersion estimates will be more reliable, 
+so you could consider using a smaller prior.n, although I would hesitate to use a prior.n less than 5. 
+
+
+From Bioconductor Digest, Vol 118, Issue 5, Gordon writes:
+
+Dear Dorota,
+
+The important settings are prior.df and trend.
+
+prior.n and prior.df are related through prior.df = prior.n * residual.df,
+and your experiment has residual.df = 36 - 12 = 24.  So the old setting of
+prior.n=10 is equivalent for your data to prior.df = 240, a very large
+value.  Going the other way, the new setting of prior.df=10 is equivalent
+to prior.n=10/24.
+
+To recover old results with the current software you would use
+
+  estimateTagwiseDisp(object, prior.df=240, trend="none")
+
+To get the new default from old software you would use
+
+  estimateTagwiseDisp(object, prior.n=10/24, trend=TRUE)
+
+Actually the old trend method is equivalent to trend="loess" in the new
+software. You should use plotBCV(object) to see whether a trend is
+required.
+
+Note you could also use
+
+  prior.n = getPriorN(object, prior.df=10)
+
+to map between prior.df and prior.n.
+
+----
+
+**Attributions**
+
+edgeR - edgeR_ 
+
+VOOM/limma - limma_VOOM_ 
+
+DESeq2 - DESeq2_ for details
+
+See above for Bioconductor package documentation for packages exposed in Galaxy by this tool and app store package.
+
+Galaxy_ (that's what you are using right now!) for gluing everything together 
+
+Otherwise, all code and documentation comprising this tool was written by Ross Lazarus and is 
+licensed to you under the LGPL_ like other rgenetics artefacts
+
+.. _LGPL: http://www.gnu.org/copyleft/lesser.html
+.. _HTSeq: http://www-huber.embl.de/users/anders/HTSeq/doc/index.html
+.. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
+.. _DESeq2: http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
+.. _limma_VOOM: http://www.bioconductor.org/packages/release/bioc/html/limma.html
+.. _Galaxy: http://getgalaxy.org
+</help>
+
+</tool>
+
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/differential_count_models/test-data/edgeRtest1out.html	Wed Aug 07 01:58:28 2013 -0400
@@ -0,0 +1,733 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> 
+        <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> 
+        <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> 
+        <meta name="generator" content="Galaxy rgToolFactory.py tool output - see http://g2.trac.bx.psu.edu/" /> 
+        <title></title> 
+        <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> 
+        </head> 
+        <body> 
+        <div class="toolFormBody"> 
+        
+<div class="infomessage">Galaxy Tool "DifferentialCounts" run at 07/08/2013 15:46:55</div><br/>
+<div class="toolFormTitle">DESeq2 images and outputs</div>
+(Click on a thumbnail image to download the corresponding original PDF image)<br/>
+<div><table class="simple" cellpadding="2" cellspacing="2">
+<tr>
+<td><a href="DESeq2_MA_plot.pdf"><img src="DESeq2_MA_plot.png" title="Click to download a PDF of DESeq2_MA_plot.pdf" hspace="5" width="400" 
+                           alt="Image called DESeq2_MA_plot.pdf"/></a></td>
+
+<td><a href="DESeq2_PCA_plot.pdf"><img src="DESeq2_PCA_plot.png" title="Click to download a PDF of DESeq2_PCA_plot.pdf" hspace="5" width="400" 
+                           alt="Image called DESeq2_PCA_plot.pdf"/></a></td>
+
+<td><a href="DESeq2_dispersion_estimates.pdf"><img src="DESeq2_dispersion_estimates.png" title="Click to download a PDF of DESeq2_dispersion_estimates.pdf" hspace="5" width="400" 
+                           alt="Image called DESeq2_dispersion_estimates.pdf"/></a></td>
+</tr>
+<tr>
+<td><a href="DESeq2_qqplot.pdf"><img src="DESeq2_qqplot.png" title="Click to download a PDF of DESeq2_qqplot.pdf" hspace="5" width="400" 
+                           alt="Image called DESeq2_qqplot.pdf"/></a></td>
+
+<td><a href="DESeq2_sample_distance_plot.pdf"><img src="DESeq2_sample_distance_plot.png" title="Click to download a PDF of DESeq2_sample_distance_plot.pdf" hspace="5" width="400" 
+                           alt="Image called DESeq2_sample_distance_plot.pdf"/></a></td>
+
+<td>&nbsp;</td>
+</tr></table></div>
+
+<div class="toolFormTitle">DESeq2 log output</div>
+
+<pre>
+
+# DESeq top 50
+
+                     Contig     baseMean log2FoldChange     lfcSE        pvalue          padj  NReads                                                                                               URL
+
+Mir192               Mir192 271352.97636       6.965264 0.2150593 4.096936e-230 4.576278e-227 2325567               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
+
+Mir122a             Mir122a  10112.31117      10.312083 0.3292695 2.649323e-215 1.479647e-212   90428             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a>
+
+Mir149               Mir149    810.35429      -6.911118 0.2341392 1.735537e-191 6.461982e-189    6164               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a>
+
+Mir23a               Mir23a   1289.18043      -3.104086 0.1191688 1.424246e-149 3.977206e-147   10118               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a>
+
+Mir181d             Mir181d    275.22797      -3.581172 0.1778187  3.329371e-90  7.437816e-88    2139             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a>
+
+Mir204               Mir204    347.57397      -7.284200 0.3771119  3.959336e-83  7.370965e-81    2601               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a>
+
+Mir23b               Mir23b   2028.55377      -2.065110 0.1085802  1.182361e-80  1.886711e-78   16387               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23b'>Mir23b</a>
+
+Mir27a               Mir27a   2788.72629      -3.016676 0.1688167  2.036708e-71  2.843754e-69   21886               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a>
+
+Mir195               Mir195    519.86200      -3.152795 0.1784796  7.838123e-70  9.727982e-68    3962               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a>
+
+Mir194-2           Mir194-2    391.65678       5.222911 0.3099275  1.013490e-63  1.132068e-61    3570           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a>
+
+Mir208b             Mir208b   1649.77924     -11.396172 0.6771238  1.464479e-63  1.487112e-61   14756             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a>
+
+Mir10b               Mir10b  27820.40551      -5.071453 0.3044889  2.754493e-62  2.563974e-60  197340               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a>
+
+Mir181c             Mir181c   2765.96510      -3.660964 0.2275711  3.141153e-58  2.698975e-56   23605             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a>
+
+Mir208a             Mir208a    616.76981     -10.356524 0.6559217  3.688385e-56  2.942804e-54    4638             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a>
+
+Mir490               Mir490    220.99790      -8.059660 0.5142876  2.369067e-55  1.764165e-53    1741               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a>
+
+Mir203               Mir203    772.92882       1.990849 0.1274099  4.877239e-55  3.404923e-53    6739               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir203'>Mir203</a>
+
+Mir215               Mir215    152.78082      -3.004380 0.1939090  3.822339e-54  2.511502e-52    1182               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'>Mir215</a>
+
+Dnm3os               Dnm3os    179.61643      -3.278392 0.2166491  9.922020e-52  6.157165e-50    1401               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'>Dnm3os</a>
+
+Mir214               Mir214    134.69038      -3.216444 0.2154916  2.230148e-50  1.311093e-48    1048               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a>
+
+Mir21                 Mir21  26121.31011       2.963903 0.2008617  2.817434e-49  1.573537e-47  229120                 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a>
+
+Mir1948             Mir1948    263.89527       7.074045 0.4867225  7.374030e-48  3.922282e-46    2404             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a>
+
+Mir27b               Mir27b  76478.05753      -1.904653 0.1312889  1.088626e-47  5.527251e-46  625308               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27b'>Mir27b</a>
+
+Rabggtb             Rabggtb   2257.19195       1.988368 0.1401741  1.134862e-45  5.511484e-44   19535             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a>
+
+Mir499               Mir499    712.45950     -10.577061 0.7528467  7.766408e-45  3.614616e-43    6527               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a>
+
+Mir101b             Mir101b   6846.19683       3.791681 0.2809666  1.670548e-41  7.464007e-40   59019             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a>
+
+Mir132               Mir132    106.46062      -2.797928 0.2083376  4.046163e-41  1.738294e-39     857               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'>Mir132</a>
+
+Mir143hg           Mir143hg 180217.77425      -2.169143 0.1685614  6.764675e-38  2.798571e-36 1407364           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143hg'>Mir143hg</a>
+
+Mir143               Mir143 179219.35960      -2.170303 0.1696199  1.746403e-37  6.966899e-36 1399819               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143'>Mir143</a>
+
+Mir155               Mir155     57.66182      -3.788079 0.3056585  2.845488e-35  1.096004e-33     463               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a>
+
+Mir322               Mir322    899.53469      -3.126011 0.2622595  9.363374e-33  3.486296e-31    7074               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a>
+
+Mir378               Mir378    483.21548      -2.994300 0.2577321  3.343457e-31  1.204723e-29    4075               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a>
+
+Mir24-2             Mir24-2    424.48288      -2.712674 0.2361028  1.491830e-30  5.049617e-29    3470             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'>Mir24-2</a>
+
+Mir3074-2         Mir3074-2    424.48288      -2.712674 0.2361028  1.491830e-30  5.049617e-29    3470         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'>Mir3074-2</a>
+
+Mir199b             Mir199b     47.84725      -5.294373 0.4644474  4.215162e-30  1.384805e-28     370             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a>
+
+Mir802               Mir802    166.83414       8.816580 0.7782636  9.478527e-30  3.025004e-28    1514               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a>
+
+Mir125b-2         Mir125b-2    493.08516      -2.919341 0.2631193  1.324797e-28  4.110551e-27    3837         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a>
+
+Mir301               Mir301    260.53406      -1.676984 0.1526772  4.570133e-28  1.379686e-26    2119               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir301'>Mir301</a>
+
+Snord104           Snord104   3851.90119       2.386573 0.2173857  4.847914e-28  1.425032e-26   33458           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a>
+
+Mir150               Mir150    553.20599      -2.836881 0.2595088  8.127991e-28  2.327940e-26    4229               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir150'>Mir150</a>
+
+Mir148a             Mir148a 118994.46955       2.678852 0.2481801  3.675045e-27  1.026256e-25 1002397             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'>Mir148a</a>
+
+5430416N02Rik 5430416N02Rik     62.15966       3.089960 0.2941123  8.101331e-26  2.207119e-24     564 <a href='http://www.genecards.org/index.php?path=/Search/keyword/5430416N02Rik'>5430416N02Rik</a>
+
+Mir193               Mir193     45.70861       4.991530 0.4814098  3.446492e-25  9.166027e-24     421               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193'>Mir193</a>
+
+Mir3073             Mir3073     98.93199       8.208709 0.7944742  5.036320e-25  1.308272e-23     904             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a>
+
+Mir125b-1         Mir125b-1     79.01988      -3.020660 0.2937360  8.355633e-25  2.121191e-23     609         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-1'>Mir125b-1</a>
+
+2610203C20Rik 2610203C20Rik     79.17666      -3.023491 0.2948614  1.136165e-24  2.820214e-23     610 <a href='http://www.genecards.org/index.php?path=/Search/keyword/2610203C20Rik'>2610203C20Rik</a>
+
+Mir181a-1         Mir181a-1     59.53826      -3.151487 0.3211628  9.923707e-23  2.409735e-21     506         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-1'>Mir181a-1</a>
+
+Mir184               Mir184     32.23796      -4.865023 0.4962776  1.092606e-22  2.596683e-21     247               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'>Mir184</a>
+
+Mir199a-2         Mir199a-2     44.84878      -3.422216 0.3545647  4.826269e-22  1.123113e-20     352         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199a-2'>Mir199a-2</a>
+
+Snord91a           Snord91a    168.95251       2.700421 0.2835464  1.670595e-21  3.808275e-20    1437           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord91a'>Snord91a</a>
+
+Mir200b             Mir200b     87.13638       5.940702 0.6338554  7.094881e-21  1.584996e-19     888             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200b'>Mir200b</a>
+
+
+</pre>
+
+<div class="toolFormTitle">DifferentialCounts log output</div>
+
+<pre>
+
+Loading required package: gtools
+
+Loading required package: gdata
+
+gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
+
+gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
+
+Attaching package: ‘gdata’
+
+The following object is masked from ‘package:stats’:
+
+    nobs
+
+The following object is masked from ‘package:utils’:
+
+    object.size
+
+Loading required package: caTools
+
+Loading required package: grid
+
+Loading required package: KernSmooth
+
+KernSmooth 2.23 loaded
+
+Copyright M. P. Wand 1997-2009
+
+Loading required package: MASS
+
+Attaching package: ‘gplots’
+
+The following object is masked from ‘package:stats’:
+
+    lowess
+
+Loading required package: methods
+
+Loading required package: limma
+
+Loading required package: splines
+
+Loading required package: DESeq2
+
+Loading required package: GenomicRanges
+
+Loading required package: BiocGenerics
+
+Loading required package: parallel
+
+Attaching package: ‘BiocGenerics’
+
+The following object is masked from ‘package:parallel’:
+
+    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
+
+The following object is masked from ‘package:gdata’:
+
+    combine
+
+The following object is masked from ‘package:stats’:
+
+    xtabs
+
+The following object is masked from ‘package:base’:
+
+    anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist
+
+Loading required package: IRanges
+
+Attaching package: ‘IRanges’
+
+The following object is masked from ‘package:gplots’:
+
+    space
+
+The following object is masked from ‘package:caTools’:
+
+    runmean
+
+The following object is masked from ‘package:gdata’:
+
+    trim
+
+Loading required package: Biobase
+
+Welcome to Bioconductor
+
+    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.
+
+Loading required package: lattice
+
+Loading required package: Rcpp
+
+Loading required package: RcppArmadillo
+
+Attaching package: ‘DESeq2’
+
+The following object is masked from ‘package:limma’:
+
+    plotMA
+
+gene-wise dispersion estimates
+
+mean-dispersion relationship
+
+final dispersion estimates
+
+you had estimated dispersions, replacing these
+
+gene-wise dispersion estimates
+
+mean-dispersion relationship
+
+final dispersion estimates
+
+you had estimated dispersions, replacing these
+
+gene-wise dispersion estimates
+
+mean-dispersion relationship
+
+final dispersion estimates
+
+Warning messages:
+
+1: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group ==  :
+
+  Outlier (-Inf) in boxplot 1 is not drawn
+
+2: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group ==  :
+
+  Outlier (-Inf) in boxplot 3 is not drawn
+
+3: In bxp(list(stats = c(-0.430723026286372, -0.127900608036896, 0.474159383291067,  :
+
+  some notches went outside hinges ('box'): maybe set notch=FALSE
+
+4: In par(defpar) : calling par(new=TRUE) with no plot
+
+
+</pre>
+
+<div class="toolFormTitle">VOOM images and outputs</div>
+(Click on a thumbnail image to download the corresponding original PDF image)<br/>
+<div><table class="simple" cellpadding="2" cellspacing="2">
+<tr>
+<td><a href="VOOM_mean_variance_plot.pdf"><img src="VOOM_mean_variance_plot.png" title="Click to download a PDF of VOOM_mean_variance_plot.pdf" hspace="5" width="400" 
+                           alt="Image called VOOM_mean_variance_plot.pdf"/></a></td>
+
+<td><a href="VOOM_qqplot.pdf"><img src="VOOM_qqplot.png" title="Click to download a PDF of VOOM_qqplot.pdf" hspace="5" width="400" 
+                           alt="Image called VOOM_qqplot.pdf"/></a></td>
+</tr>
+
+</table></div>
+
+<div class="toolFormTitle">VOOM log output</div>
+
+<pre>
+
+# VOOM top 50
+
+                         ID      logFC    AveExpr          t      P.Value    adj.P.Val         B  NReads                                                                                               URL
+
+Mir192               Mir192   6.948883 14.6763803  42.722954 2.301199e-16 2.625668e-13 27.266471 2325567               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
+
+Mir208a             Mir208a -11.015018  3.9395538 -23.252407 1.118938e-12 6.383542e-10 17.208662    4638             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a>
+
+Mir122a             Mir122a  10.426125  8.1698641  21.722912 2.859682e-12 1.087633e-09 17.760171   90428             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a>
+
+Mir149               Mir149  -7.030463  6.3160807 -20.883835 4.915491e-12 1.402144e-09 17.277609    6164               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a>
+
+Mir208b             Mir208b -12.433228  4.6076218 -19.592458 1.179199e-11 2.690931e-09 15.683666   14756             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a>
+
+Mir10b               Mir10b  -5.130915 12.2628672 -18.242023 3.124991e-11 4.963978e-09 16.221503  197340               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a>
+
+Mir143hg           Mir143hg  -2.249221 16.2444825 -18.082481 3.521739e-11 4.963978e-09 16.026695 1407364           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143hg'>Mir143hg</a>
+
+Mir143               Mir143  -2.251067 16.2358599 -18.081481 3.524391e-11 4.963978e-09 16.026084 1399819               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143'>Mir143</a>
+
+Mir499               Mir499 -11.567529  3.7874598 -17.942086 3.915496e-11 4.963978e-09 14.821741    6527               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a>
+
+Mir802               Mir802   9.158434  2.9157675  17.316522 6.338616e-11 7.232360e-09 14.381577    1514               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a>
+
+Mir3073             Mir3073   8.420542  2.5457189  16.702657 1.033066e-10 1.036045e-08 13.985845     904             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a>
+
+Mir148a             Mir148a   2.638213 15.4435820  16.548188 1.171186e-10 1.036045e-08 14.814792 1002397             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'>Mir148a</a>
+
+Mir101b             Mir101b   3.765722 10.8508440  16.538566 1.180419e-10 1.036045e-08 14.900027   59019             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a>
+
+Mir490               Mir490  -8.474378  3.7506957 -16.259650 1.484816e-10 1.210125e-08 13.424617    1741               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a>
+
+Mir21                 Mir21   2.938537 13.1642917  15.375404 3.148335e-10 2.394833e-08 13.867698  229120                 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a>
+
+Mir181c             Mir181c  -3.742560  9.6295577 -15.242361 3.537063e-10 2.522368e-08 13.810405   23605             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a>
+
+Mir204               Mir204  -7.684425  4.7751735 -15.033484 4.254268e-10 2.855364e-08 12.822427    2601               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a>
+
+Mir23a               Mir23a  -3.165768  8.7896592 -14.631179 6.110682e-10 3.873493e-08 13.269174   10118               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a>
+
+Mir181d             Mir181d  -3.636211  6.3713218 -14.317073 8.157508e-10 4.898798e-08 12.956333    2139             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a>
+
+Mir133b             Mir133b  -6.493549  1.2544862 -13.969968 1.129934e-09 6.446275e-08 11.982684     159             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133b'>Mir133b</a>
+
+Mir27a               Mir27a  -3.106935  9.9255796 -13.838251 1.281011e-09 6.960160e-08 12.513086   21886               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a>
+
+Mir194-2           Mir194-2   5.264136  6.0897615  13.044012 2.792884e-09 1.448491e-07 11.715753    3570           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a>
+
+Mir195               Mir195  -3.216595  7.4509350 -12.869478 3.332788e-09 1.653353e-07 11.587523    3962               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a>
+
+Mir27b               Mir27b  -1.976376 15.0957731 -11.756036 1.082197e-08 5.144946e-07 10.127719  625308               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27b'>Mir27b</a>
+
+Mir378               Mir378  -3.097393  7.3832049 -11.684163 1.171371e-08 5.346138e-07 10.329692    4075               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a>
+
+Snord104           Snord104   2.337374 10.6109024  11.495675 1.444482e-08 6.339052e-07 10.023395   33458           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a>
+
+Mir1983             Mir1983  -5.895500  0.9931851 -11.445812 1.527548e-08 6.441605e-07  9.749260     101             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1983'>Mir1983</a>
+
+Mir322               Mir322  -3.296618  8.2153415 -11.415362 1.580762e-08 6.441605e-07 10.008472    7074               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a>
+
+Mir200a             Mir200a   6.191561  1.7981309  11.322172 1.756229e-08 6.909853e-07  9.662295     264             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200a'>Mir200a</a>
+
+Mir215               Mir215  -3.045873  5.7544234 -11.148134 2.141822e-08 8.082459e-07  9.753268    1182               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'>Mir215</a>
+
+Dnm3os               Dnm3os  -3.363344  5.8607432 -11.092261 2.283960e-08 8.082459e-07  9.689496    1401               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'>Dnm3os</a>
+
+Mir182               Mir182   4.903995  7.1511683  11.074468 2.331304e-08 8.082459e-07  9.658842    7189               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a>
+
+Mir181a-2         Mir181a-2  -3.048298  6.9414651 -11.072128 2.337609e-08 8.082459e-07  9.644017    2817         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-2'>Mir181a-2</a>
+
+Mir1948             Mir1948   7.195525  4.5513493  11.005492 2.524936e-08 8.473388e-07  9.341794    2404             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a>
+
+Mir214               Mir214  -3.280874  5.4784451 -10.768257 3.332555e-08 1.086413e-06  9.318504    1048               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a>
+
+Mir153               Mir153  -5.963803  1.4386315 -10.727082 3.498742e-08 1.093990e-06  9.035569     140               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir153'>Mir153</a>
+
+Cyp3a25             Cyp3a25   6.318200  1.4888933  10.698226 3.620443e-08 1.093990e-06  9.024973     226             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp3a25'>Cyp3a25</a>
+
+Gm5441               Gm5441  -5.982176  1.4484953 -10.692891 3.643436e-08 1.093990e-06  9.000362     142               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5441'>Gm5441</a>
+
+Mir125b-2         Mir125b-2  -3.077678  7.4316058 -10.446668 4.893073e-08 1.431538e-06  8.884250    3837         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a>
+
+Mir133a-1         Mir133a-1  -5.144671  0.5903264 -10.358205 5.447229e-08 1.553822e-06  8.575535      60         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133a-1'>Mir133a-1</a>
+
+1110038B12Rik 1110038B12Rik   2.226702 10.8487089  10.194609 6.655312e-08 1.852125e-06  8.439308   37066 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1110038B12Rik'>1110038B12Rik</a>
+
+Mir132               Mir132  -2.847559  5.3211839 -10.110952 7.380297e-08 2.004981e-06  8.531491     857               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'>Mir132</a>
+
+Rabggtb             Rabggtb   1.935779  9.9874171   9.928995 9.262821e-08 2.457879e-06  8.133384   19535             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a>
+
+Mir504               Mir504  -5.256127  0.6221088  -9.892894 9.693595e-08 2.513725e-06  8.068853      69               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir504'>Mir504</a>
+
+Mir150               Mir150  -2.938531  7.6297870  -9.842102 1.033602e-07 2.620755e-06  8.116464    4229               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir150'>Mir150</a>
+
+Mir199b             Mir199b  -5.752816  2.8805143  -9.823920 1.057683e-07 2.623514e-06  7.979387     370             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a>
+
+Mir23b               Mir23b  -2.124129  9.8141190  -9.806316 1.081569e-07 2.625681e-06  7.979464   16387               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23b'>Mir23b</a>
+
+Mir24-2             Mir24-2  -2.833979  7.3083691  -9.767192 1.136724e-07 2.646944e-06  8.030550    3470             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'>Mir24-2</a>
+
+Mir3074-2         Mir3074-2  -2.833979  7.3083691  -9.767192 1.136724e-07 2.646944e-06  8.030550    3470         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'>Mir3074-2</a>
+
+Mir155               Mir155  -3.906600  3.9899000  -9.732173 1.188627e-07 2.712448e-06  8.046518     463               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a>
+
+
+</pre>
+
+<div class="toolFormTitle">edgeR images and outputs</div>
+(Click on a thumbnail image to download the corresponding original PDF image)<br/>
+<div><table class="simple" cellpadding="2" cellspacing="2">
+<tr>
+<td><a href="edgeR_BCV_vs_abundance.pdf"><img src="edgeR_BCV_vs_abundance.png" title="Click to download a PDF of edgeR_BCV_vs_abundance.pdf" hspace="5" width="400" 
+                           alt="Image called edgeR_BCV_vs_abundance.pdf"/></a></td>
+
+<td><a href="edgeR_GoodnessofFit.pdf"><img src="edgeR_GoodnessofFit.png" title="Click to download a PDF of edgeR_GoodnessofFit.pdf" hspace="5" width="400" 
+                           alt="Image called edgeR_GoodnessofFit.pdf"/></a></td>
+
+<td><a href="edgeR_MDSplot.pdf"><img src="edgeR_MDSplot.png" title="Click to download a PDF of edgeR_MDSplot.pdf" hspace="5" width="400" 
+                           alt="Image called edgeR_MDSplot.pdf"/></a></td>
+</tr>
+<tr>
+<td><a href="edgeR_qqplot.pdf"><img src="edgeR_qqplot.png" title="Click to download a PDF of edgeR_qqplot.pdf" hspace="5" width="400" 
+                           alt="Image called edgeR_qqplot.pdf"/></a></td>
+
+<td><a href="edgeR_raw_norm_counts_box.pdf"><img src="edgeR_raw_norm_counts_box.png" title="Click to download a PDF of edgeR_raw_norm_counts_box.pdf" hspace="5" width="400" 
+                           alt="Image called edgeR_raw_norm_counts_box.pdf"/></a></td>
+
+<td><a href="edgeR_smearplot.pdf"><img src="edgeR_smearplot.png" title="Click to download a PDF of edgeR_smearplot.pdf" hspace="5" width="400" 
+                           alt="Image called edgeR_smearplot.pdf"/></a></td>
+</tr>
+<tr>
+<td><a href="edgeR_top_100_heatmap.pdf"><img src="edgeR_top_100_heatmap.png" title="Click to download a PDF of edgeR_top_100_heatmap.pdf" hspace="5" width="400" 
+                           alt="Image called edgeR_top_100_heatmap.pdf"/></a></td>
+
+<td>&nbsp;</td><td>&nbsp;</td>
+</tr></table></div>
+
+<div class="toolFormTitle">edgeR log output</div>
+
+<pre>
+
+[1] prior.df = 8
+
+[1] "No GLM fit outlier genes found\n"
+
+[1] Common Dispersion = 0.228651460998105 CV =  0.478175136323613 getPriorN =  3.33333333333333
+
+[1] heart liver
+
+[1] "Raw sample read totals 2443751,1644652,1682104,1806045,1440960,1341813,2888924,1428365"
+
+[1] raw contig counts by sample:
+
+ liver_X11706Liv_CAAA liver_X11700Liv_ATTC liver_X11698Liv_ACTG liver_X11699Liv_ATGA heart_X11706He_AGTTC heart_X11699He_GGCTA heart_X11698He_TAGCT heart_X11700He_CTTGT
+
+ Min.   :0.0043       Min.   :0.0043       Min.   :0.0043       Min.   :0.0043       Min.   :0.0043       Min.   :0.0043       Min.   :0.0043       Min.   :0.0043      
+
+ 1st Qu.:0.3032       1st Qu.:0.0043       1st Qu.:0.3032       1st Qu.:0.0043       1st Qu.:0.0043       1st Qu.:0.0043       1st Qu.:0.0043       1st Qu.:0.0043      
+
+ Median :0.7789       Median :0.6031       Median :0.6998       Median :0.6031       Median :0.4786       Median :0.4786       Median :0.4786       Median :0.4786      
+
+ Mean   :1.0519       Mean   :1.0343       Mean   :0.9855       Mean   :0.9966       Mean   :0.9210       Mean   :0.9428       Mean   :1.0205       Mean   :0.9753      
+
+ 3rd Qu.:1.5410       3rd Qu.:1.6335       3rd Qu.:1.4473       3rd Qu.:1.5534       3rd Qu.:1.5770       3rd Qu.:1.5855       3rd Qu.:1.7161       3rd Qu.:1.6022      
+
+ Max.   :5.8209       Max.   :5.6905       Max.   :5.7999       Max.   :5.7215       Max.   :5.3609       Max.   :5.3589       Max.   :5.6967       Max.   :5.3702      
+
+ NA's   :650          NA's   :969          NA's   :664          NA's   :886          NA's   :902          NA's   :957          NA's   :821          NA's   :950         
+
+[1] normalised contig counts by sample:
+
+ liver_X11706Liv_CAAA liver_X11700Liv_ATTC liver_X11698Liv_ACTG liver_X11699Liv_ATGA heart_X11706He_AGTTC heart_X11699He_GGCTA heart_X11698He_TAGCT heart_X11700He_CTTGT
+
+ Min.   :-Inf         Min.   :-Inf         Min.   :-Inf         Min.   :-Inf         Min.   :-Inf         Min.   :-Inf         Min.   :-Inf         Min.   :-Inf        
+
+ 1st Qu.:   0         1st Qu.:-Inf         1st Qu.:   0         1st Qu.:-Inf         1st Qu.:-Inf         1st Qu.:-Inf         1st Qu.:-Inf         1st Qu.:-Inf        
+
+ Median :   0         Median :   0         Median :   0         Median :   0         Median :   0         Median :   0         Median :   0         Median :   0        
+
+ Mean   :-Inf         Mean   :-Inf         Mean   :-Inf         Mean   :-Inf         Mean   :-Inf         Mean   :-Inf         Mean   :-Inf         Mean   :-Inf        
+
+ 3rd Qu.:   1         3rd Qu.:   1         3rd Qu.:   1         3rd Qu.:   1         3rd Qu.:   1         3rd Qu.:   1         3rd Qu.:   1         3rd Qu.:   1        
+
+ Max.   :   6         Max.   :   6         Max.   :   6         Max.   :   5         Max.   :   5         Max.   :   5         Max.   :   6         Max.   :   5        
+
+[1] Using ncol rawrs= 8
+
+[1] # edgeR Top tags\n
+
+                       Name      logFC    logCPM        LR        PValue   adj.p.value Dispersion totreads                                                                                               URL
+
+Mir208a             Mir208a -11.840751  8.465017 594.16946 3.104543e-131 3.542284e-128 0.05171220     4638             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a>
+
+Mir149               Mir149  -7.008984  8.861767 484.30321 2.473909e-107 1.411365e-104 0.04959937     6164               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a>
+
+Mir208b             Mir208b -13.291635  9.905945 417.69758  7.737463e-93  2.942815e-90 0.10508096    14756             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a>
+
+Mir122a             Mir122a  10.514683 12.478088 415.17429  2.740525e-92  7.817349e-90 0.10803882    90428             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a>
+
+Mir204               Mir204  -7.498162  7.634507 341.30678  3.313430e-76  7.561247e-74 0.06907958     2601               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a>
+
+Mir499               Mir499 -13.577454  8.700078 325.79199  7.930755e-73  1.508165e-70 0.12042284     6527               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a>
+
+Mir490               Mir490  -8.534394  6.991023 303.17184  6.710366e-68  1.093790e-65 0.07949711     1741               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a>
+
+Mir192               Mir192   6.953853 17.169364 217.22867  3.638307e-49  5.189135e-47 0.12700995  2325567               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
+
+Mir802               Mir802  11.440805  6.593380 212.88059  3.231644e-48  4.097007e-46 0.12273671     1514               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a>
+
+Mir1948             Mir1948   7.418142  7.252734 195.66958  1.840248e-44  2.099723e-42 0.12060221     2404             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a>
+
+Mir194-2           Mir194-2   5.298950  7.811522 191.85588  1.250960e-43  1.297587e-41 0.08670751     3570           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a>
+
+Mir23a               Mir23a  -3.153807  9.529402 177.53185  1.676248e-40  1.593833e-38 0.04442763    10118               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a>
+
+Mir181c             Mir181c  -3.767686 10.639598 169.87390  7.883295e-39  6.919107e-37 0.06368883    23605             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a>
+
+Mir3073             Mir3073  10.686337  5.859950 164.86740  9.778593e-38  7.969554e-36 0.14069249      904             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a>
+
+Mir181d             Mir181d  -3.643963  7.300371 162.18591  3.767663e-37  2.865936e-35 0.05729574     2139             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a>
+
+Mir195               Mir195  -3.203683  8.215089 150.20548  1.563314e-34  1.114838e-32 0.05235020     3962               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a>
+
+Mir10b               Mir10b  -5.182616 13.946466 147.24793  6.926819e-34  4.649118e-32 0.12268790   197340               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a>
+
+Mir101b             Mir101b   3.759962 11.863187 136.31359  1.703812e-31  1.080028e-29 0.07961343    59019             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a>
+
+Mir378               Mir378  -3.115599  8.119617 126.76408  2.092233e-29  1.256441e-27 0.05942391     4075               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a>
+
+Mir27a               Mir27a  -3.064687 10.642480 124.98911  5.117477e-29  2.919520e-27 0.06113852    21886               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a>
+
+Mir182               Mir182   5.057509  8.846381 123.17765  1.275060e-28  6.927826e-27 0.13653707     7189               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a>
+
+Mir322               Mir322  -3.194159  9.012888 107.34926  3.732413e-25  1.935765e-23 0.07536483     7074               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a>
+
+Mir199b             Mir199b  -5.520119  4.792610 102.10724  5.259607e-24  2.609223e-22 0.13417024      370             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a>
+
+Mir181a-2         Mir181a-2  -3.000177  7.637692 101.38361  7.578821e-24  3.603098e-22 0.06896654     2817         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-2'>Mir181a-2</a>
+
+Mir125b-2         Mir125b-2  -2.987759  8.144514  91.72544  9.957640e-22  4.488356e-20 0.07737381     3837         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a>
+
+Dnm3os               Dnm3os  -3.331215  6.686950  91.67250  1.022763e-21  4.488356e-20 0.08810497     1401               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'>Dnm3os</a>
+
+Mir184               Mir184  -5.111350  4.234160  84.35542  4.133639e-20  1.686711e-18 0.13502324      247               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'>Mir184</a>
+
+Mir215               Mir215  -3.058208  6.447966  84.35278  4.139167e-20  1.686711e-18 0.08138517     1182               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'>Mir215</a>
+
+Mir133b             Mir133b  -8.383611  3.584760  83.96681  5.031517e-20  1.960318e-18 0.17482280      159             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133b'>Mir133b</a>
+
+Mir150               Mir150  -2.883446  8.307765  83.91918  5.154210e-20  1.960318e-18 0.08008123     4229               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir150'>Mir150</a>
+
+Mir3074-2         Mir3074-2  -2.778308  7.935651  83.74839  5.619282e-20  2.040616e-18 0.07424646     3470         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'>Mir3074-2</a>
+
+Mir24-2             Mir24-2  -2.778307  7.935651  83.71222  5.723024e-20  2.040616e-18 0.07427992     3470             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'>Mir24-2</a>
+
+Mir193               Mir193   5.176579  4.801090  83.19222  7.445011e-20  2.574169e-18 0.14794861      421               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193'>Mir193</a>
+
+Scarna17           Scarna17   2.182159  9.244479  81.91330  1.421894e-19  4.771710e-18 0.04982909     9224           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Scarna17'>Scarna17</a>
+
+Mir214               Mir214  -3.271172  6.271755  80.43948  2.997458e-19  9.771712e-18 0.09566584     1048               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a>
+
+Snord104           Snord104   2.330488 11.053611  79.50529  4.809369e-19  1.524303e-17 0.05915990    33458           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a>
+
+Mir200a             Mir200a   7.201555  4.139422  77.35503  1.428304e-18  4.365755e-17 0.19287764      264             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200a'>Mir200a</a>
+
+Mir200b             Mir200b   6.525423  5.752604  77.31985  1.453976e-18  4.365755e-17 0.26237966      888             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200b'>Mir200b</a>
+
+Mir21                 Mir21   2.923147 13.825255  75.51798  3.620938e-18  1.059357e-16 0.09395834   229120                 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a>
+
+Mir203               Mir203   1.956427  8.767610  75.17870  4.299815e-18  1.226522e-16 0.04381710     6739               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir203'>Mir203</a>
+
+Mir155               Mir155  -3.886731  5.068563  73.81316  8.587210e-18  2.389758e-16 0.12522673      463               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a>
+
+Cyp3a25             Cyp3a25   8.681501  3.972085  72.29680  1.851471e-17  5.029829e-16 0.23125383      226             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp3a25'>Cyp3a25</a>
+
+Rabggtb             Rabggtb   1.934093 10.298211  72.02043  2.129809e-17  5.651422e-16 0.04596646    19535             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a>
+
+Mir23b               Mir23b  -2.100584 10.184110  71.44225  2.854935e-17  7.403367e-16 0.05416378    16387               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23b'>Mir23b</a>
+
+Snord52             Snord52   2.207491 10.217554  71.27974  3.100027e-17  7.860292e-16 0.05941483    18059             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord52'>Snord52</a>
+
+Gm5441               Gm5441  -6.881248  3.538457  70.05615  5.764004e-17  1.429724e-15 0.20097284      142               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5441'>Gm5441</a>
+
+Mir153               Mir153  -6.857671  3.517446  69.37600  8.137282e-17  1.975455e-15 0.20158808      140               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir153'>Mir153</a>
+
+Mir132               Mir132  -2.858294  5.938312  64.52507  9.531204e-16  2.265647e-14 0.09274248      857               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'>Mir132</a>
+
+1110038B12Rik 1110038B12Rik   2.195962 11.253090  62.92015  2.152583e-15  5.012443e-14 0.06712174    37066 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1110038B12Rik'>1110038B12Rik</a>
+
+Snord91a           Snord91a   2.654072  6.557504  62.40549  2.795431e-15  6.379174e-14 0.08637410     1437           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord91a'>Snord91a</a>
+
+[1] # 416 tags significant at adj p= 0.05
+
+
+</pre>
+
+<div class="toolFormTitle">Other images and outputs</div>
+(Click on a thumbnail image to download the corresponding original PDF image)<br/>
+<div><table class="simple" cellpadding="2" cellspacing="2">
+<tr>
+<td><a href="Filtering_rowsum_bar_charts.pdf"><img src="Filtering_rowsum_bar_charts.png" title="Click to download a PDF of Filtering_rowsum_bar_charts.pdf" hspace="5" width="400" 
+                           alt="Image called Filtering_rowsum_bar_charts.pdf"/></a></td>
+
+<td><a href="Venn_significant_genes_overlap.pdf"><img src="Venn_significant_genes_overlap.png" title="Click to download a PDF of Venn_significant_genes_overlap.pdf" hspace="5" width="400" 
+                           alt="Image called Venn_significant_genes_overlap.pdf"/></a></td>
+</tr>
+<tr>
+<td><a href="sample_counts_histogram.pdf"><img src="sample_counts_histogram.png" title="Click to download a PDF of sample_counts_histogram.pdf" hspace="5" width="400" 
+                           alt="Image called sample_counts_histogram.pdf"/></a></td>
+
+<td>&nbsp;</td>
+</tr></table></div>
+
+<div class="toolFormTitle">Other log output</div>
+
+<pre>
+
+## Toolfactory generated command line = Rscript - None None
+
+Got TCols=1 5 6 7; CCols=2 3 4 8
+
+[1] # Quantiles for non-zero row counts:
+
+       0%       10%       20%       30%       40%       50%       60%       70%       80%       90%      100% 
+
+      1.0       1.0       2.0       3.0       4.0       8.0      13.0      24.0      86.6     753.0 2325567.0 
+
+[1] Read 3242 contigs. Removed 1494 with no reads. After filtering at count quantile =0.3, there are 1141 contigs
+
+[1] "@@ using genecards substitution for urls"
+
+[1] # urls
+
+[1] <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610005C13Rik'>0610005C13Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610007N19Rik'>0610007N19Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610008F07Rik'>0610008F07Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610009L18Rik'>0610009L18Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610012G03Rik'>0610012G03Rik</a>
+
+[6] <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610031O16Rik'>0610031O16Rik</a>
+
+[1] # Total low count contigs per sample =  170,67,203,86,145,111,155,120
+
+[1] Using samples: liver_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam,liver_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam,liver_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam,liver_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam,heart_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam,heart_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam,heart_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam,heart_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam
+
+[1] Using design matrix:
+
+  (Intercept) groupliver
+
+1           1          1
+
+2           1          1
+
+3           1          1
+
+4           1          1
+
+5           1          0
+
+6           1          0
+
+7           1          0
+
+8           1          0
+
+attr(,"assign")
+
+[1] 0 1
+
+attr(,"contrasts")
+
+attr(,"contrasts")$group
+
+[1] contr.treatment
+
+R version 3.0.1 (2013-05-16)
+
+Platform: x86_64-unknown-linux-gnu (64-bit)
+
+locale:
+
+ [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C               LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8     LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8    LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       
+
+attached base packages:
+
+ [1] parallel  splines   methods   grid      stats     graphics  grDevices utils     datasets  base     
+
+other attached packages:
+
+ [1] RColorBrewer_1.0-5      DESeq2_1.0.18           RcppArmadillo_0.3.900.7 Rcpp_0.10.4             lattice_0.20-15         Biobase_2.20.1          GenomicRanges_1.12.4    IRanges_1.18.2          BiocGenerics_0.6.0      edgeR_3.2.4             limma_3.16.7            gplots_2.11.3           MASS_7.3-28             KernSmooth_2.23-10      caTools_1.14            gdata_2.13.2            gtools_3.0.0            stringr_0.6.2          
+
+loaded via a namespace (and not attached):
+
+ [1] annotate_1.38.0      AnnotationDbi_1.22.6 bitops_1.0-5         DBI_0.2-7            genefilter_1.42.0    locfit_1.5-9.1       RSQLite_0.11.4       stats4_3.0.1         survival_2.37-4      XML_3.98-1.1         xtable_1.7-1        
+
+
+</pre>
+
+<div class="toolFormTitle">All output files available for downloading</div>
+
+<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>
+
+<tr><td><a href="DESeq2.log">DESeq2.log</a></td><td>10.0 KB</td></tr>
+<tr class="odd_row"><td><a href="DESeq2_MA_plot.pdf">DESeq2_MA_plot.pdf</a></td><td>14.7 KB</td></tr>
+<tr><td><a href="DESeq2_PCA_plot.pdf">DESeq2_PCA_plot.pdf</a></td><td>4.9 KB</td></tr>
+<tr class="odd_row"><td><a href="DESeq2_dispersion_estimates.pdf">DESeq2_dispersion_estimates.pdf</a></td><td>188.4 KB</td></tr>
+<tr><td><a href="DESeq2_qqplot.pdf">DESeq2_qqplot.pdf</a></td><td>14.4 KB</td></tr>
+<tr class="odd_row"><td><a href="DESeq2_sample_distance_plot.pdf">DESeq2_sample_distance_plot.pdf</a></td><td>9.5 KB</td></tr>
+<tr><td><a href="DifferentialCounts.Rscript">DifferentialCounts.Rscript</a></td><td>27.1 KB</td></tr>
+<tr class="odd_row"><td><a href="DifferentialCounts_error.log">DifferentialCounts_error.log</a></td><td>3.1 KB</td></tr>
+<tr><td><a href="DifferentialCounts_runner.log">DifferentialCounts_runner.log</a></td><td>3.2 KB</td></tr>
+<tr class="odd_row"><td><a href="Filtering_rowsum_bar_charts.pdf">Filtering_rowsum_bar_charts.pdf</a></td><td>6.3 KB</td></tr>
+<tr><td><a href="VOOM.log">VOOM.log</a></td><td>10.1 KB</td></tr>
+<tr class="odd_row"><td><a href="VOOM_mean_variance_plot.pdf">VOOM_mean_variance_plot.pdf</a></td><td>16.7 KB</td></tr>
+<tr><td><a href="VOOM_qqplot.pdf">VOOM_qqplot.pdf</a></td><td>17.6 KB</td></tr>
+<tr class="odd_row"><td><a href="Venn_significant_genes_overlap.pdf">Venn_significant_genes_overlap.pdf</a></td><td>9.7 KB</td></tr>
+<tr><td><a href="edgeR.log">edgeR.log</a></td><td>13.1 KB</td></tr>
+<tr class="odd_row"><td><a href="edgeR_BCV_vs_abundance.pdf">edgeR_BCV_vs_abundance.pdf</a></td><td>17.4 KB</td></tr>
+<tr><td><a href="edgeR_GoodnessofFit.pdf">edgeR_GoodnessofFit.pdf</a></td><td>13.1 KB</td></tr>
+<tr class="odd_row"><td><a href="edgeR_MDSplot.pdf">edgeR_MDSplot.pdf</a></td><td>4.9 KB</td></tr>
+<tr><td><a href="edgeR_qqplot.pdf">edgeR_qqplot.pdf</a></td><td>15.2 KB</td></tr>
+<tr class="odd_row"><td><a href="edgeR_raw_norm_counts_box.pdf">edgeR_raw_norm_counts_box.pdf</a></td><td>7.8 KB</td></tr>
+<tr><td><a href="edgeR_smearplot.pdf">edgeR_smearplot.pdf</a></td><td>16.6 KB</td></tr>
+<tr class="odd_row"><td><a href="edgeR_top_100_heatmap.pdf">edgeR_top_100_heatmap.pdf</a></td><td>11.3 KB</td></tr>
+<tr><td><a href="sample_counts_histogram.pdf">sample_counts_histogram.pdf</a></td><td>11.0 KB</td></tr>
+</table></div><br/>
+</div></body></html>
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/differential_count_models/test-data/edgeRtest1out.xls	Wed Aug 07 01:58:28 2013 -0400
@@ -0,0 +1,1142 @@
+ID	logFC	AveExpr	t	P.Value	adj.P.Val	B	NReads	URL
+Mir192	6.94888256843679	14.6763802609023	42.7229535356942	2.30119906424271e-16	2.62566813230094e-13	27.2664713266936	2325567	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
+Mir208a	-11.0150177152075	3.93955375669227	-23.2524066836307	1.11893807599952e-12	6.38354172357727e-10	17.2086622097974	4638	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a>
+Mir122a	10.4261254701779	8.16986409392255	21.7229119192922	2.85968233611017e-12	1.08763251516723e-09	17.760171141852	90428	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a>
+Mir149	-7.03046258655617	6.31608073609863	-20.8838348040628	4.91549082404237e-12	1.40214375755809e-09	17.2776088871455	6164	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a>
+Mir208b	-12.4332279840446	4.60762179736006	-19.5924575126382	1.17919871718875e-11	2.69093147262473e-09	15.6836663826186	14756	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a>
+Mir10b	-5.1309149063532	12.2628671946242	-18.2420234752943	3.12499057505143e-11	4.96397841614262e-09	16.2215027882858	197340	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a>
+Mir143hg	-2.24922058313374	16.2444825488726	-18.0824813146443	3.52173903971276e-11	4.96397841614262e-09	16.0266951625541	1407364	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143hg'>Mir143hg</a>
+Mir143	-2.25106712131643	16.235859869169	-18.0814805993441	3.524391092512e-11	4.96397841614262e-09	16.0260836456534	1399819	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143'>Mir143</a>
+Mir499	-11.5675289490546	3.78745976580796	-17.9420857279689	3.91549568319751e-11	4.96397841614262e-09	14.8217405828874	6527	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a>
+Mir802	9.15843445824816	2.91576747878654	17.3165224121399	6.33861560587965e-11	7.23236040630868e-09	14.381577240531	1514	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a>
+Mir3073	8.42054159318439	2.54571889776166	16.7026571721381	1.03306635740721e-10	1.03604453339228e-08	13.9858447292853	904	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a>
+Mir148a	2.63821345578617	15.4435819751152	16.5481882215215	1.17118649515038e-10	1.03604453339228e-08	14.8147917664862	1002397	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'>Mir148a</a>
+Mir101b	3.76572195114225	10.8508440499081	16.5385659719288	1.1804188373444e-10	1.03604453339228e-08	14.9000274171241	59019	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a>
+Mir490	-8.47437764634465	3.75069567634692	-16.2596504905533	1.48481644820999e-10	1.21012540529114e-08	13.4246171016517	1741	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a>
+Mir21	2.93853744034991	13.1642916950886	15.3754036511693	3.14833456057776e-10	2.39483315574615e-08	13.8676979022068	229120	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a>
+Mir181c	-3.74256009957124	9.62955774646065	-15.2423608550805	3.53706264458683e-10	2.52236779842098e-08	13.8104046176901	23605	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a>
+Mir204	-7.68442507149438	4.77517348536933	-15.0334839919296	4.2542677795722e-10	2.85536443323052e-08	12.8224274879526	2601	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a>
+Mir23a	-3.16576837850821	8.78965917558611	-14.6311785109623	6.11068192724496e-10	3.87349337721472e-08	13.2691736804205	10118	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a>
+Mir181d	-3.63621106402109	6.37132182424908	-14.3170733565449	8.15750840848868e-10	4.89879847057136e-08	12.9563328312209	2139	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a>
+Mir133b	-6.49354876170712	1.25448620431148	-13.969968060601	1.12993427319653e-09	6.44627502858619e-08	11.9826837063041	159	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133b'>Mir133b</a>
+Mir27a	-3.10693537246128	9.92557960348829	-13.8382510839158	1.28101104196848e-09	6.96015999469543e-08	12.5130856443239	21886	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a>
+Mir194-2	5.26413595786074	6.08976151689046	13.0440120203829	2.79288399641768e-09	1.44849119996026e-07	11.7157527118771	3570	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a>
+Mir195	-3.21659545049586	7.4509349905835	-12.869478368273	3.33278798407795e-09	1.65335264775345e-07	11.5875227405737	3962	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a>
+Mir27b	-1.97637614533106	15.0957731023791	-11.75603589654	1.08219717999805e-08	5.14494575990741e-07	10.1277185662145	625308	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27b'>Mir27b</a>
+Mir378	-3.09739319841142	7.38320489393809	-11.6841625470748	1.17137125863851e-08	5.34613842442616e-07	10.3296922348831	4075	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a>
+Snord104	2.33737428989677	10.6109023861403	11.4956750870273	1.44448164322638e-08	6.33905213431269e-07	10.0233949189609	33458	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a>
+Mir1983	-5.89550024150745	0.993185099223749	-11.4458119994178	1.52754786535047e-08	6.44160462853232e-07	9.74926029381244	101	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1983'>Mir1983</a>
+Mir322	-3.29661750880005	8.21534154356388	-11.4153616003567	1.58076187203247e-08	6.44160462853232e-07	10.0084716002011	7074	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a>
+Mir200a	6.19156065085543	1.79813092499896	11.3221723123067	1.75622912046568e-08	6.9098531946598e-07	9.66229453831667	264	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200a'>Mir200a</a>
+Mir215	-3.04587333807051	5.75442336214621	-11.1481336257529	2.14182153707674e-08	8.08245865886245e-07	9.75326755116029	1182	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'>Mir215</a>
+Dnm3os	-3.36334357719079	5.86074322417943	-11.0922610835813	2.28395969947309e-08	8.08245865886245e-07	9.68949616901383	1401	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'>Dnm3os</a>
+Mir182	4.90399541739044	7.1511683493624	11.0744681203078	2.33130367310143e-08	8.08245865886245e-07	9.65884218207857	7189	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a>
+Mir181a-2	-3.04829832099813	6.94146510070354	-11.0721276255975	2.33760855164295e-08	8.08245865886245e-07	9.64401697815694	2817	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-2'>Mir181a-2</a>
+Mir1948	7.19552540631629	4.5513492833967	11.0054920626234	2.52493600829575e-08	8.47338819254543e-07	9.34179361673467	2404	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a>
+Mir214	-3.28087400431203	5.47844506177362	-10.7682572190636	3.3325545851092e-08	1.0864127947456e-06	9.3185039394887	1048	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a>
+Mir153	-5.9638030672045	1.43863148956561	-10.7270821099311	3.49874201497232e-08	1.09398957489501e-06	9.03556928822473	140	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir153'>Mir153</a>
+Cyp3a25	6.3181999278218	1.48889330889732	10.698226339624	3.62044305804168e-08	1.09398957489501e-06	9.02497280953977	226	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp3a25'>Cyp3a25</a>
+Gm5441	-5.98217559924296	1.44849534030207	-10.6928905219357	3.64343591989574e-08	1.09398957489501e-06	9.00036161342169	142	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5441'>Gm5441</a>
+Mir125b-2	-3.07767777869034	7.43160584496732	-10.4466676018996	4.89307304174606e-08	1.43153752323904e-06	8.88425047860251	3837	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a>
+Mir133a-1	-5.1446707114636	0.590326422018506	-10.3582048674166	5.44722862183524e-08	1.5538219643785e-06	8.57553468686339	60	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133a-1'>Mir133a-1</a>
+1110038B12Rik	2.2267024913641	10.8487089345135	10.1946092089644	6.6553123680318e-08	1.85212473461568e-06	8.43930767784171	37066	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1110038B12Rik'>1110038B12Rik</a>
+Mir132	-2.84755882904953	5.32118389129247	-10.1109518209472	7.38029688527407e-08	2.00498065383279e-06	8.53149092529729	857	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'>Mir132</a>
+Rabggtb	1.93577875106629	9.98741711657765	9.92899544482161	9.26282059254969e-08	2.45787867351144e-06	8.13338404178509	19535	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a>
+Mir504	-5.25612736011945	0.622108812393712	-9.89289391617729	9.69359452558378e-08	2.51372530765707e-06	8.06885345567596	69	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir504'>Mir504</a>
+Mir150	-2.93853062743745	7.62978695478889	-9.84210172881295	1.0336018288322e-07	2.62075485932786e-06	8.11646444295523	4229	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir150'>Mir150</a>
+Mir199b	-5.75281586680568	2.88051428778536	-9.82392040215114	1.05768314120536e-07	2.62351405242461e-06	7.97938664656761	370	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a>
+Mir23b	-2.12412853458823	9.81411903779331	-9.80631552439508	1.08156895246613e-07	2.62568122290182e-06	7.97946421769546	16387	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23b'>Mir23b</a>
+Mir24-2	-2.83397931671342	7.30836912335631	-9.76719188905173	1.13672435494913e-07	2.64694385509584e-06	8.03055035937719	3470	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'>Mir24-2</a>
+Mir3074-2	-2.83397931671342	7.30836912335631	-9.76719188905173	1.13672435494913e-07	2.64694385509584e-06	8.03055035937719	3470	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'>Mir3074-2</a>
+Mir155	-3.90660012470502	3.98990000150695	-9.73217278591154	1.18862734970705e-07	2.71244761203149e-06	8.04651834419983	463	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a>
+Snord52	2.24297808473649	9.80695706696893	9.65508926768283	1.31194241930095e-07	2.93514960867135e-06	7.78317356265822	18059	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord52'>Snord52</a>
+Scarna17	2.22135685073443	8.84690751573681	9.60031550237377	1.4077767610154e-07	3.08898708522803e-06	7.75116302071276	9224	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Scarna17'>Scarna17</a>
+Mir201	-5.13478218238105	0.574435171385817	-9.36375298852343	1.91556946938131e-07	4.12389578219637e-06	7.45101629313275	63	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir201'>Mir201</a>
+Mir184	-5.19740389169544	2.57741455998865	-9.28503096123923	2.12504578894189e-07	4.42570763295992e-06	7.34294491810118	247	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'>Mir184</a>
+Snord91a	2.64601724328653	5.9737770599439	9.28208610647144	2.1333384733812e-07	4.42570763295992e-06	7.45176303063652	1437	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord91a'>Snord91a</a>
+Mir193	4.93970055277848	3.14663535122407	9.21323530535893	2.33732739541295e-07	4.76230456815389e-06	7.28752724029761	421	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193'>Mir193</a>
+Mir470	5.07947201153691	1.71052510073336	8.84181308472679	3.85901653714362e-07	7.72480327873838e-06	6.83971839651152	157	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir470'>Mir470</a>
+0610031O16Rik	4.84298796174609	0.739739561937192	8.8004727262221	4.08431072700958e-07	8.03482506813436e-06	6.77016207746292	78	<a href='http://www.genecards.org/index.php?path=/Search/keyword/0610031O16Rik'>0610031O16Rik</a>
+Mir203	1.9396775595845	8.44497102033975	8.70156015908293	4.6818189744087e-07	9.05416177932259e-06	6.53224466632053	6739	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir203'>Mir203</a>
+1810019D21Rik	5.37088028736873	1.02158093294187	8.63951664435106	5.10331246821015e-07	9.70479921037964e-06	6.58253399607689	117	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1810019D21Rik'>1810019D21Rik</a>
+D7Ertd143e	4.74135480360802	0.690096187370941	8.59182875086527	5.45451616539556e-07	1.02026277782235e-05	6.49996146777963	73	<a href='http://www.genecards.org/index.php?path=/Search/keyword/D7Ertd143e'>D7Ertd143e</a>
+Mir181a-1	-3.20886334319296	4.33388500974742	-8.528721562826	5.95908204570219e-07	1.09666332486229e-05	6.48742379588458	506	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-1'>Mir181a-1</a>
+Mir547	-4.64199116509563	0.384583900671288	-8.48569977551612	6.33121735643368e-07	1.14665381010966e-05	6.34288346197563	42	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir547'>Mir547</a>
+Mir3102	-4.82802034015575	1.26816340424779	-8.40617041640129	7.08539703084848e-07	1.26319343940595e-05	6.2533959548051	87	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3102'>Mir3102</a>
+Mir194-1	3.86792676846218	4.28030595336869	8.2361953191898	9.03449017918911e-07	1.5859005068392e-05	6.08687440143381	635	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-1'>Mir194-1</a>
+Mir199a-2	-3.62193724804755	3.76746624824118	-8.22528846947687	9.17754251311817e-07	1.58660242537391e-05	6.07294487982063	352	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199a-2'>Mir199a-2</a>
+Mir375	4.36561952992499	1.70304479419652	8.20239976081094	9.48559026077637e-07	1.61538186381281e-05	5.9804850351652	123	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir375'>Mir375</a>
+Mir128-1	-2.79500838795041	4.68404652058909	-8.16636754121193	9.99287948408945e-07	1.67674639578619e-05	5.95537435854342	527	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir128-1'>Mir128-1</a>
+Mir1a-1	-4.50930254765404	0.235845136893643	-8.15352480043541	1.01805558742015e-06	1.68348032644405e-05	5.89233114702952	42	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1a-1'>Mir1a-1</a>
+Mir17hg	1.26324530315481	13.08692945461	8.08792426896809	1.11990826888155e-06	1.80004069127122e-05	5.39248242771111	145451	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir17hg'>Mir17hg</a>
+Mir92-1	1.26323093975761	13.0869221993444	8.08780961117952	1.12009543453336e-06	1.80004069127122e-05	5.39230857078851	145450	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir92-1'>Mir92-1</a>
+Mir881	4.55329779507755	0.622217688176746	7.98090604480001	1.30985575977083e-06	2.06385233899717e-05	5.68307629847666	64	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir881'>Mir881</a>
+Mir125b-1	-3.19780406116102	4.7293501044755	-7.96524973476641	1.340381181277e-06	2.06385233899717e-05	5.66721192306587	609	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-1'>Mir125b-1</a>
+2610203C20Rik	-3.20042083590071	4.73071629949528	-7.96367997663051	1.3434829565975e-06	2.06385233899717e-05	5.66487879544241	610	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2610203C20Rik'>2610203C20Rik</a>
+Scnn1b	-4.63822537309801	0.37290502628334	-7.9570799219013	1.35660758479218e-06	2.06385233899717e-05	5.63911983957	45	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Scnn1b'>Scnn1b</a>
+Mir193b	-3.19095319216208	3.51292960275358	-7.90681185253976	1.46112366345347e-06	2.19360802631633e-05	5.62073482323402	260	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193b'>Mir193b</a>
+Mir183	4.30421971951602	3.92737361468754	7.78136892736858	1.76081314682182e-06	2.60215226213659e-05	5.44000583749589	563	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir183'>Mir183</a>
+5430416N02Rik	3.07746071410873	4.3937689770433	7.77455061595853	1.77885956570249e-06	2.60215226213659e-05	5.40856341816749	564	<a href='http://www.genecards.org/index.php?path=/Search/keyword/5430416N02Rik'>5430416N02Rik</a>
+Mir125a	-2.6112312467571	10.9299667279975	-7.67497504879118	2.06586606398761e-06	2.98373820127831e-05	4.87458713303236	37867	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125a'>Mir125a</a>
+Mir200b	6.64163006978911	3.12821174098826	7.58298811849222	2.37461716273863e-06	3.38679772835598e-05	5.13195387121669	888	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200b'>Mir200b</a>
+C430049B03Rik	-1.92074554462898	10.5496297843175	-7.55549117760725	2.4760890707944e-06	3.48792299972396e-05	4.70418935748661	25716	<a href='http://www.genecards.org/index.php?path=/Search/keyword/C430049B03Rik'>C430049B03Rik</a>
+Terc	4.24682289892723	0.87844372666952	7.3826580782883	3.2281439398588e-06	4.49184418948646e-05	4.83681905205792	66	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Terc'>Terc</a>
+Mir871	5.21513327520529	2.43957936484213	7.24439581531717	4.00226877508459e-06	5.50191406309821e-05	4.63418699567578	290	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir871'>Mir871</a>
+Mir30e	-1.90475431278526	13.2693114305891	-7.14894534136424	4.6492913699815e-06	6.28199839913465e-05	3.89856793405104	186796	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir30e'>Mir30e</a>
+Mir24-1	-3.10183666628555	3.10602318965769	-7.13671325687185	4.73984945200915e-06	6.28199839913465e-05	4.48008371426601	189	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-1'>Mir24-1</a>
+Mir3074-1	-3.10183666628555	3.10602318965769	-7.13671325687185	4.73984945200915e-06	6.28199839913465e-05	4.48008371426601	189	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-1'>Mir3074-1</a>
+Mir592	4.27837071128313	0.882966518707851	7.13005059451541	4.78995495814825e-06	6.28199839913465e-05	4.46386515426502	70	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir592'>Mir592</a>
+Serpina4-ps1	6.28609584979245	1.44994282762173	7.10887070838901	4.95297318411398e-06	6.42198000349325e-05	4.43976042902202	295	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Serpina4-ps1'>Serpina4-ps1</a>
+Mirlet7e	-1.98704484524714	6.38418687649397	-6.91936550313624	6.69984149789542e-06	8.58934735853783e-05	3.9044291222869	1576	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mirlet7e'>Mirlet7e</a>
+Mir3470b	4.76222273641772	1.545054677666	6.90067154705821	6.90430035193184e-06	8.75311855728247e-05	4.11927719036494	132	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3470b'>Mir3470b</a>
+Mir497	-2.37449282835512	5.72555109896591	-6.88407718002354	7.09129622786183e-06	8.89139450108829e-05	3.89837376299718	963	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir497'>Mir497</a>
+Mir30d	-1.6250750764544	13.1824457426439	-6.86162843142705	7.35278174335401e-06	9.11904779257275e-05	3.42562585807056	161730	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir30d'>Mir30d</a>
+Mir107	1.66807649183652	7.69910580818381	6.8393447582273	7.62239107335082e-06	9.35177227386374e-05	3.6976878474277	3843	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir107'>Mir107</a>
+Mir301	-1.74763355751926	6.9632575863254	-6.82958967456103	7.7436706688371e-06	9.39949812036503e-05	3.72033936484245	2119	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir301'>Mir301</a>
+Mir455	2.46320289727146	5.30404932290074	6.81532109954182	7.92473126605604e-06	9.51801934165257e-05	3.83331724079003	895	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir455'>Mir455</a>
+Mir429	4.86439995826456	3.23263249974835	6.78791698606005	8.28507245768243e-06	9.84715382730797e-05	3.94480735955982	499	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir429'>Mir429</a>
+1700003L19Rik	-3.76057540139707	-0.126261497218445	-6.63064169305684	1.07147990447279e-05	0.000126033542791258	3.68122560260964	23	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1700003L19Rik'>1700003L19Rik</a>
+Mir99a	-2.28512022818228	9.92572736694444	-6.62442810768864	1.08249668655068e-05	0.000126033542791258	3.2109507357583	17575	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir99a'>Mir99a</a>
+Mir145	-1.97697703068737	8.78484403570673	-6.5439327901519	1.23647594606541e-05	0.000141146069525717	3.13555880659816	7539	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir145'>Mir145</a>
+Mir34b	-4.12275476924448	0.708468030075098	-6.54365850253687	1.23703829558034e-05	0.000141146069525717	3.55740492991767	54	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir34b'>Mir34b</a>
+Mir31	2.28911995870681	6.51541747970347	6.52931766820141	1.26681737242473e-05	0.000143112734845209	3.25621845009615	2078	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir31'>Mir31</a>
+Mir181b-1	-3.60801009779468	-0.132126628141882	-6.46494720684188	1.41005553764556e-05	0.000157732683181724	3.42410398459059	19	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181b-1'>Mir181b-1</a>
+Gm6307	-4.1578316997704	0.656018151435715	-6.45273564502753	1.43909587108892e-05	0.000159418290185675	3.41462429299529	52	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm6307'>Gm6307</a>
+Scarna6	1.69929242985022	7.02301841351445	6.42269285853436	1.51324405034754e-05	0.000166020332831399	3.03238527080513	2398	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Scarna6'>Scarna6</a>
+Snord45b	1.94022355970573	6.80826479898751	6.39728013438808	1.57909283820436e-05	0.000171594755084873	3.00447879542696	2199	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord45b'>Snord45b</a>
+Mir212	-2.84645310030162	3.44913875490104	-6.35557690856707	1.6937466935156e-05	0.000182317450688802	3.21240862806012	232	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir212'>Mir212</a>
+Mir488	-4.10203604485773	1.24180834532503	-6.29103817686794	1.88870111723183e-05	0.000201402614463693	3.15543310741006	78	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir488'>Mir488</a>
+Mir1943	-2.71589064856915	3.44876720857909	-6.23580114025192	2.07423167962376e-05	0.000219138735782473	3.00834314558259	215	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1943'>Mir1943</a>
+Gas5	1.24087717560169	10.5129034284973	6.13133629490868	2.4792457454819e-05	0.000259524715192188	2.31915097100889	24887	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gas5'>Gas5</a>
+Mir1960	-3.55886465849503	0.603332307653829	-6.02805967736536	2.96173517543744e-05	0.000307212712288556	2.72737825973636	36	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1960'>Mir1960</a>
+Snord72	1.83422077226714	4.99202771858388	6.01300538064759	3.03988327484681e-05	0.000312478091585605	2.48059356064701	603	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord72'>Snord72</a>
+Mir126	-1.4123938474776	14.7113257499272	-5.9690966101592	3.28038341776394e-05	0.000334189060684701	1.77670178050375	420720	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir126'>Mir126</a>
+Mir181b-2	-3.5537298874584	2.37784481058975	-5.74465057345259	4.86143755138839e-05	0.000490876127976474	2.24688113349229	154	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181b-2'>Mir181b-2</a>
+4930581F22Rik	3.25147651228939	0.329341147921603	5.72231806379132	5.05741508633493e-05	0.000506185141535803	2.2176701707354	33	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930581F22Rik'>4930581F22Rik</a>
+Taf1d	1.56967838004803	6.27598295057893	5.62971411199061	5.96235762303463e-05	0.000591569569381088	1.67884064404776	1421	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Taf1d'>Taf1d</a>
+Mir324	-2.38077905852261	3.65370681185719	-5.61738196066422	6.09504435595697e-05	0.000599521173288526	1.9104544791018	248	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir324'>Mir324</a>
+Mtmr2	-2.30493988089979	4.77764446891153	-5.57410629776523	6.58554908247018e-05	0.000642231752401579	1.7123130370103	580	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mtmr2'>Mtmr2</a>
+Mir137	3.41092416262533	0.0324356592441258	5.50287186084007	7.48455682327983e-05	0.000723718587742567	1.84456682895684	29	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir137'>Mir137</a>
+Snhg1	0.975366701589908	11.1969347059892	5.49575538415102	7.5811401213261e-05	0.000726897552809502	1.12394645028672	37837	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snhg1'>Snhg1</a>
+Mir34a	-2.05826883405221	3.36051649740781	-5.47484354411999	7.87253643157781e-05	0.000748547005702523	1.67723038143596	180	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir34a'>Mir34a</a>
+Mir298	-3.44904214184284	0.481437816526014	-5.39740371005322	9.05725273791661e-05	0.000854076477187012	1.66441956376117	37	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir298'>Mir298</a>
+Mir30b	-1.37954359870678	9.2115221848988	-5.37206514503938	9.4840390621554e-05	0.000886990866386828	1.00959570224732	10011	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir30b'>Mir30b</a>
+2310001H17Rik	3.60260656982356	0.877139295086231	5.35615735698035	9.76262576906534e-05	0.000902593356272145	1.57720822721783	54	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2310001H17Rik'>2310001H17Rik</a>
+Pex16	3.10814004056272	0.242483417469106	5.35355087544425	9.80907766676126e-05	0.000902593356272145	1.58678494520955	30	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Pex16'>Pex16</a>
+Mir741	3.33919133389387	0.432231427661093	5.2950378042311	0.000109146860855228	0.000996292545886519	1.47796989545021	36	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir741'>Mir741</a>
+Gm6313	-3.15860344908017	-0.430119305523511	-5.24231069726794	0.000120220067795944	0.00108865950281883	1.40353714409938	15	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm6313'>Gm6313</a>
+Mir328	-1.36488724959	7.2282210636054	-5.23221518519415	0.000122470141866871	0.00110030261315039	0.870852174596449	2362	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir328'>Mir328</a>
+Snord33	1.25647224562943	7.71222650703403	5.19862342341357	0.000130277220055511	0.00116129928190108	0.778490918357933	3442	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord33'>Snord33</a>
+Rpph1	1.87063945690961	4.43992987975591	5.19124070458341	0.000132061294296316	0.0011680770293961	1.05386997375291	430	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Rpph1'>Rpph1</a>
+Mir291a	3.17904342101315	-0.0791999402663102	5.18540568400292	0.000133489301957871	0.00117026083393732	1.2956738181937	24	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir291a'>Mir291a</a>
+Mir186	-1.38629871411117	10.176089899221	-5.181881716386	0.000134359482248719	0.00117026083393732	0.594672202880173	18235	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir186'>Mir186</a>
+Gm16596	-3.02811906442667	-0.421976649282355	-5.15901843295933	0.000140150118907224	0.00121144913388744	1.25840752971795	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm16596'>Gm16596</a>
+Mirlet7i	-1.21381140575271	10.6031742297066	-5.15326347701587	0.000141648110216644	0.00121519168238489	0.514620675402163	26242	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mirlet7i'>Mirlet7i</a>
+Sra1	2.97648314190951	-0.188256184051246	5.14486604509538	0.000143863812461334	0.00122498962700285	1.22868620554498	19	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Sra1'>Sra1</a>
+Mir700	-3.05275751205424	3.03686027981893	-5.10658051111472	0.00015443097639702	0.00130522773384445	1.06937466394294	177	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir700'>Mir700</a>
+Mir30c-1	-1.44640830149114	5.51774362365196	-5.09058727395353	0.000159080836478697	0.0013266290585589	0.730639691134108	732	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir30c-1'>Mir30c-1</a>
+Mir674	-1.94702895981213	4.45877434664642	-5.08988436247691	0.000159288502210841	0.0013266290585589	0.846234772297753	392	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir674'>Mir674</a>
+Snord45c	1.44139263505882	6.31780757188042	5.0752407566119	0.000163679307853258	0.00135146340163194	0.643628779392595	1427	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord45c'>Snord45c</a>
+Ank1	-1.70157147221109	10.9929711198162	-5.07209350467361	0.000164639275045433	0.00135146340163194	0.337810380148678	33776	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Ank1'>Ank1</a>
+Mirlet7b	-1.09478453248563	9.30463614623057	-5.06223764308063	0.000167683437276746	0.00136662001380548	0.418305977430397	10012	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mirlet7b'>Mirlet7b</a>
+0610008F07Rik	3.20935973501609	0.342617899865038	5.04843460516125	0.000172045196108449	0.00139222389191305	1.0441746904328	34	<a href='http://www.genecards.org/index.php?path=/Search/keyword/0610008F07Rik'>0610008F07Rik</a>
+Snord4a	1.57395983217788	5.94089477513251	5.00029990452424	0.000188198499627571	0.00151221470475393	0.535941755206456	1151	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord4a'>Snord4a</a>
+Mir3107	-1.70018651164628	9.99212523723331	-4.97672369154541	0.000196676176463643	0.00155838553711817	0.215189363582583	16873	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3107'>Mir3107</a>
+Mir486	-1.70018651164628	9.99212523723331	-4.97672369154541	0.000196676176463643	0.00155838553711817	0.215189363582583	16873	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir486'>Mir486</a>
+Mir100	-1.97076444192024	8.99815411447499	-4.96949043197095	0.000199355724522589	0.00156872332193292	0.262493038912075	8837	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir100'>Mir100</a>
+6430411K18Rik	-3.18910263916585	-0.373872894349982	-4.91488268129579	0.000220845557812913	0.00170486995980212	0.826251830470595	17	<a href='http://www.genecards.org/index.php?path=/Search/keyword/6430411K18Rik'>6430411K18Rik</a>
+Mir433	-3.18910263916585	-0.373872894349982	-4.91488268129579	0.000220845557812913	0.00170486995980212	0.826251830470595	17	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir433'>Mir433</a>
+Mir190	-2.07544392773473	3.1544454577673	-4.91417324518583	0.000221140012314386	0.00170486995980212	0.671557118650327	163	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir190'>Mir190</a>
+Mir668	-2.84374273013661	-0.157703843092941	-4.86996462339487	0.000240314465841743	0.00184026043976798	0.746753746471687	15	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir668'>Mir668</a>
+0610012G03Rik	2.84115361016785	-0.244188556172649	4.84933497977366	0.000249843031682205	0.00190047266099598	0.705829411755822	17	<a href='http://www.genecards.org/index.php?path=/Search/keyword/0610012G03Rik'>0610012G03Rik</a>
+Mirlet7d	-1.19906882560952	10.0080528514984	-4.83828196963314	0.000255108219097298	0.00192767203966899	-0.0535917366982233	16847	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mirlet7d'>Mirlet7d</a>
+Mir320	-1.40563797109219	6.563348272824	-4.77568906174122	0.000287168062262582	0.00215564973053688	0.0467165593444996	1651	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir320'>Mir320</a>
+Snord66	1.15430111322029	8.03351541888005	4.75658981303321	0.00029775850741536	0.00222053893438514	-0.0877963597335594	4212	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord66'>Snord66</a>
+Hgd	4.54425664237216	0.975547692617975	4.73952572490202	0.000307561641064749	0.00225560361403978	0.450492806487889	137	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Hgd'>Hgd</a>
+Aqp9	4.93135714830861	0.753510541775538	4.73814880056307	0.000308367063909922	0.00225560361403978	0.445426512401092	161	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Aqp9'>Aqp9</a>
+Mir221	-1.08377350661343	8.47402248983799	-4.73470478811828	0.000310391167513083	0.00225560361403978	-0.161171563827692	5659	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir221'>Mir221</a>
+Atf5	3.74327970750113	0.168725495917353	4.73192727585554	0.00031203354916423	0.00225560361403978	0.467422722695712	50	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Atf5'>Atf5</a>
+Ahsg	7.43012370228481	2.43819500653074	4.73140267365542	0.000312344759875797	0.00225560361403978	0.392509485594371	1524	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Ahsg'>Ahsg</a>
+Cyp2d13	3.62058562658928	0.099076105394318	4.71784217799444	0.000320501474638856	0.00229995083372915	0.445950346991055	44	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp2d13'>Cyp2d13</a>
+Mir292	3.55331832828793	0.0808135496327816	4.67052458846538	0.000350727059524427	0.00250112234323357	0.360392052911509	41	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir292'>Mir292</a>
+Proc	4.16579682989808	0.376893953921531	4.63475223165321	0.000375520073648099	0.00266129443498435	0.275862327084029	83	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Proc'>Proc</a>
+2610019E17Rik	1.58277820027238	5.58959301890268	4.63093795449771	0.00037826821496869	0.00266422242764985	-0.140287526130874	892	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2610019E17Rik'>2610019E17Rik</a>
+Mir379	-2.08294744907303	3.05372097245691	-4.61798165733268	0.000387758909131681	0.00271431236392177	0.128998572399559	153	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir379'>Mir379</a>
+Mir96	3.092187161072	-0.127577830654966	4.61264491367143	0.000391739223724717	0.00272545398945063	0.269031262574771	24	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir96'>Mir96</a>
+5033403H07Rik	3.03100334960097	-0.167104636116587	4.55138913141517	0.00044055961680218	0.00304390944849929	0.159657330767462	23	<a href='http://www.genecards.org/index.php?path=/Search/keyword/5033403H07Rik'>5033403H07Rik</a>
+Mir582	-4.60557103590561	3.35812677089552	-4.5486926708253	0.00044284747454065	0.00304390944849929	0.0591283272554897	566	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir582'>Mir582</a>
+Mir335	-1.27174458468766	6.43063411797007	-4.54414079104836	0.000446737391037914	0.00305225965972611	-0.393123932477534	1318	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir335'>Mir335</a>
+Gm5424	4.79310957596335	1.09020146508355	4.53505892344961	0.000454603987554657	0.00308751874880871	0.0640172708933422	181	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5424'>Gm5424</a>
+Snord96a	1.64486304749729	4.67116544357615	4.51910388563813	0.0004687711663005	0.00316489882099923	-0.255892987917286	487	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord96a'>Snord96a</a>
+Fam120b	3.09294836244015	0.400892342309139	4.51279274228026	0.000474499826623265	0.00318473118927733	0.0711882890790463	39	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Fam120b'>Fam120b</a>
+1810032O08Rik	1.41990709594509	5.47749401704587	4.44622801412284	0.000539494231805467	0.00359978314906455	-0.491596569959665	801	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1810032O08Rik'>1810032O08Rik</a>
+D830005E20Rik	-2.66421484690988	-0.635454055345691	-4.43818702356919	0.00054794279494766	0.00363489958741442	-0.0273233727843643	9	<a href='http://www.genecards.org/index.php?path=/Search/keyword/D830005E20Rik'>D830005E20Rik</a>
+Mir3057	-1.76308589999293	3.90842103747244	-4.39033832828025	0.000601107772422842	0.00396453160886973	-0.421971049333088	244	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3057'>Mir3057</a>
+Dcaf11	3.64616824902598	1.34504089418874	4.36305371925593	0.000633768357283662	0.00415591779115321	-0.228339632338981	105	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Dcaf11'>Dcaf11</a>
+Mir141	2.71262314324362	4.77357067250837	4.34309768158673	0.000658805704226011	0.00429541319155359	-0.576407055554532	835	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir141'>Mir141</a>
+Clip4	-2.70686636040313	-0.590132795422603	-4.22339289420565	0.000831845216151027	0.00538076227850526	-0.424317219340228	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Clip4'>Clip4</a>
+Atp2a2	-3.03468731889576	3.9897529348455	-4.22163834350324	0.000834701948549895	0.00538076227850526	-0.712425757555907	394	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Atp2a2'>Atp2a2</a>
+Snord11	1.70196648813426	4.30076703857411	4.20393833047899	0.000864088763598198	0.00553890606328957	-0.81986210274439	399	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord11'>Snord11</a>
+Mir1a-2	-2.99188005456984	-0.157703843092941	-4.1964183364679	0.00087689254654494	0.0055585244200432	-0.484125725482271	23	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1a-2'>Mir1a-2</a>
+Mir1b	-2.99188005456984	-0.157703843092941	-4.1964183364679	0.00087689254654494	0.0055585244200432	-0.484125725482271	23	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1b'>Mir1b</a>
+Snord95	0.986915429703335	7.67764085008967	4.16122119437911	0.000939451338082392	0.00592217666713818	-1.23233286437982	3258	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord95'>Snord95</a>
+Tardbp	2.97062100907675	0.883541928525332	4.15354257136734	0.000953695266999763	0.00597893571234467	-0.601444869463529	52	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Tardbp'>Tardbp</a>
+Mir34c	-4.34256582352703	3.19074386781529	-4.14603488500754	0.000967835650645262	0.00601077590779499	-0.705590893704782	715	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir34c'>Mir34c</a>
+Nagpa	2.44212396887249	0.350172381597785	4.14525853315587	0.000969310049986221	0.00601077590779499	-0.597611598821245	24	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Nagpa'>Nagpa</a>
+Bmp1	2.83284622628297	0.517967853857585	4.09387916064743	0.00107217035218767	0.00661268309106014	-0.708641495529353	39	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Bmp1'>Bmp1</a>
+Crem	2.33712898304139	-0.121515515943567	4.0829392931282	0.00109547464985413	0.00672008911550302	-0.694023102630085	16	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Crem'>Crem</a>
+AI506816	2.42270659752045	-0.452690836228738	4.06592993902701	0.00113274010846169	0.00690883244123217	-0.71823549330855	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/AI506816'>AI506816</a>
+Snhg12	1.2392736392255	8.22309194102909	4.06341770887408	0.0011383527598174	0.00690883244123217	-1.46153826275546	5403	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snhg12'>Snhg12</a>
+Snord99	1.60658132000619	7.61494864267921	4.05085172286681	0.00116685579559478	0.00702317443883207	-1.44229619547632	3970	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord99'>Snord99</a>
+Mir450b	-1.85261764183761	3.54483087111489	-4.0485135276699	0.00117223928473074	0.00702317443883207	-1.03659851317493	205	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir450b'>Mir450b</a>
+Mir218-1	-2.37943795492075	-0.788253108012747	-4.04703416313971	0.00117565847310861	0.00702317443883207	-0.747038393026922	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir218-1'>Mir218-1</a>
+Mir140	-0.901201558594089	9.41159056411459	-4.03552071597731	0.00120261909580773	0.00711569212542235	-1.59661829698077	10795	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir140'>Mir140</a>
+Mir483	-2.42347249247516	-0.756810762138252	-4.03017784461274	0.0012153437165189	0.00711569212542235	-0.779102255351839	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir483'>Mir483</a>
+Sqrdl	3.73159563362893	0.945260485192632	4.02973478085716	0.00121640506624817	0.00711569212542235	-0.861776345505721	102	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Sqrdl'>Sqrdl</a>
+Mir144	-2.29129119700542	9.41554506116587	-4.02892270273821	0.00121835283652175	0.00711569212542235	-1.60506726133582	13709	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir144'>Mir144</a>
+Mir210	-1.50896749399836	4.99944311707418	-4.02726966499444	0.00122232748166764	0.00711569212542235	-1.27568646998696	592	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir210'>Mir210</a>
+Mir136	-1.91584100290298	5.18425364003902	-4.01919516322722	0.00124193308478254	0.0071567962107923	-1.30273093425232	753	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir136'>Mir136</a>
+Mir3071	-1.91584100290298	5.18425364003902	-4.01919516322722	0.00124193308478254	0.0071567962107923	-1.30273093425232	753	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3071'>Mir3071</a>
+Snord43	1.12653255459757	7.42275234629614	4.00820447995329	0.00126913582767258	0.00727680391645436	-1.51733899954002	2975	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord43'>Snord43</a>
+Nlrp5-ps	3.06966395518949	-0.135132312387713	3.98319245863032	0.00133332885542151	0.00760664112017971	-0.902428549559341	34	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Nlrp5-ps'>Nlrp5-ps</a>
+4833418N02Rik	1.82386047796749	3.16360132579728	3.94914311648112	0.00142607040510993	0.00809525538423099	-1.16130756295351	170	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4833418N02Rik'>4833418N02Rik</a>
+Pknox1	2.58217103686749	-0.386376496641391	3.94009175499237	0.00145181139000837	0.00820057819801758	-0.95836656931183	16	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Pknox1'>Pknox1</a>
+Mir1843	1.0607275776375	7.37281183848222	3.92128643575477	0.00150681377235572	0.008458947103908	-1.6871582740604	2782	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1843'>Mir1843</a>
+Scarna3b	1.05890367361984	7.37450114126396	3.91942250502631	0.00151237967501948	0.008458947103908	-1.69099763322655	2784	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Scarna3b'>Scarna3b</a>
+Phyhd1	2.69871613662387	-0.324381809808589	3.91199503566496	0.00153476742516205	0.00850676625406398	-1.01680363882686	20	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Phyhd1'>Phyhd1</a>
+Gm14207	-2.37304409257741	-0.416502509079365	-3.91164184680055	0.00153584035787658	0.00850676625406398	-1.00193629125355	11	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm14207'>Gm14207</a>
+2700038G22Rik	-1.20941383309973	5.69714561045198	-3.89423392377302	0.00158967928624185	0.00876243509952633	-1.61494260853442	872	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2700038G22Rik'>2700038G22Rik</a>
+Mir1249	-1.57997335358757	3.92571996538164	-3.86749708921129	0.00167613304205796	0.00914790116608117	-1.45071018307216	240	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1249'>Mir1249</a>
+Mir680-2	2.69993600843854	2.33940488575521	3.86630244603638	0.00168010559076576	0.00914790116608117	-1.19260507987069	134	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir680-2'>Mir680-2</a>
+4732471J01Rik	2.47123788102083	1.83426864599497	3.86203852417355	0.00169436257731633	0.00914790116608117	-1.16621943210526	78	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4732471J01Rik'>4732471J01Rik</a>
+0610005C13Rik	3.75552246080227	1.36486301235638	3.86197876879019	0.00169456324819645	0.00914790116608117	-1.18181214765895	126	<a href='http://www.genecards.org/index.php?path=/Search/keyword/0610005C13Rik'>0610005C13Rik</a>
+Mir297a-3	-2.83038541581836	0.620898493219045	-3.86045228910567	0.00169969767502998	0.00914790116608117	-1.12583690632738	32	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir297a-3'>Mir297a-3</a>
+D830015G02Rik	-2.85288965105576	-0.0430116131169372	-3.8540007067199	0.00172157316996324	0.00918761905215916	-1.135758525707	19	<a href='http://www.genecards.org/index.php?path=/Search/keyword/D830015G02Rik'>D830015G02Rik</a>
+Mir190b	-2.58480150088673	0.118920372323834	-3.85352956525721	0.00172318183800356	0.00918761905215916	-1.12342997930169	19	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir190b'>Mir190b</a>
+Cacnb2	-2.36615720731133	-0.788253108012747	-3.84657108578939	0.00174711947070295	0.00927192240033519	-1.12169301350773	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Cacnb2'>Cacnb2</a>
+Mtfr1	2.77427419358368	0.492589466798896	3.83997888411189	0.001770108543009	0.00935043447950588	-1.18729669638225	40	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mtfr1'>Mtfr1</a>
+Snord1a	1.56162899910724	3.64400301591315	3.83681604346118	0.0017812471515648	0.00936313497745819	-1.45598973323054	230	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord1a'>Snord1a</a>
+Snord68	0.957663081634941	8.79334935483305	3.83464756418373	0.00178892500007527	0.00936313497745819	-1.95644313626433	7303	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord68'>Snord68</a>
+Mir878	2.41936085459412	-0.447944854953861	3.82652263259005	0.00181799260036803	0.00947182446127819	-1.16702401112308	13	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir878'>Mir878</a>
+Mir511	1.70981318188926	3.27929603694437	3.81643804724114	0.0018547387918105	0.00959956329857923	-1.44128807747474	183	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir511'>Mir511</a>
+Gm15787	2.48153800186339	-0.386376496641391	3.81519042194731	0.00185933697544786	0.00959956329857923	-1.19313192146596	14	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm15787'>Gm15787</a>
+Surf1	2.36126838851735	0.0872159088448913	3.80305260835126	0.00190467958178741	0.00978936667936682	-1.23097217655323	20	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Surf1'>Surf1</a>
+Mir1968	2.37800084613411	0.673754504632647	3.77926083620018	0.00199683807660974	0.0102052996591412	-1.28734965758831	33	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1968'>Mir1968</a>
+0610007N19Rik	-1.90120438734532	2.49555567542219	-3.77758577340756	0.00200349441161053	0.0102052996591412	-1.41487533930946	104	<a href='http://www.genecards.org/index.php?path=/Search/keyword/0610007N19Rik'>0610007N19Rik</a>
+Snhg8	1.59039445480745	3.20715500905903	3.75615085858512	0.00209068421652196	0.0106020919602291	-1.55245580151111	164	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snhg8'>Snhg8</a>
+Mir99b	-1.91682795135645	10.9172256229833	-3.75211079306552	0.0021075435523792	0.0106402973153304	-2.25375326353787	35086	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir99b'>Mir99b</a>
+Mir365-2	2.40700496454038	0.263026808334256	3.74756102414217	0.00212669484901157	0.0106896864437102	-1.33894003797924	25	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir365-2'>Mir365-2</a>
+A630019I02Rik	-2.46429396746277	-0.331334129436178	-3.72894212518103	0.00220692150206125	0.0110442869905785	-1.34913426897275	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/A630019I02Rik'>A630019I02Rik</a>
+Snora24	1.55151202645698	3.18622291582758	3.72443395692917	0.00222680324291416	0.011095120088057	-1.61270421930364	160	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora24'>Snora24</a>
+Tmem205	3.35434252485109	1.34402776298411	3.71826658220279	0.00225429637910924	0.0111803962803989	-1.43852442151233	106	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Tmem205'>Tmem205</a>
+Chka	2.66265038819564	-0.367431606769972	3.71621547263374	0.00226351581136911	0.0111803962803989	-1.38147433178837	20	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Chka'>Chka</a>
+Il15ra	3.0322333836799	1.34537734368953	3.69802409752219	0.00234697158113459	0.0115426490261835	-1.46743653610507	78	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Il15ra'>Il15ra</a>
+Mir340	1.08524047523296	8.40150339094243	3.68614126686871	0.00240316001921397	0.0117592747718197	-2.22640527546981	5906	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir340'>Mir340</a>
+Mir222	-0.989531454809674	6.83748363675873	-3.68437434098812	0.00241163040894463	0.0117592747718197	-2.12318215364121	1840	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir222'>Mir222</a>
+Snord16a	2.29129601947442	3.76378890459482	3.66271871458069	0.0025179297139219	0.0122253523556804	-1.78739319047154	368	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord16a'>Snord16a</a>
+Snora16a	1.52372874357926	4.55536943029929	3.65510898252504	0.0025563971250754	0.0123595301682671	-1.93830245300744	464	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora16a'>Snora16a</a>
+Meg3	-2.68467060880573	-0.63693223477029	-3.65193847372806	0.00257259886012651	0.0123853810101449	-1.49159048882037	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Meg3'>Meg3</a>
+Mir503	-1.62803161355467	2.50957996141068	-3.64484640281096	0.00260921685489431	0.0125088925690521	-1.68081269699905	88	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir503'>Mir503</a>
+Snord34	1.9527050627559	2.43578559807808	3.64115899694926	0.00262846334208935	0.0125484379636985	-1.64754683241552	110	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord34'>Snord34</a>
+Mir330	-1.20046349365495	3.89404790732931	-3.62347773804946	0.00272276191759244	0.0129444639498874	-1.93549975651123	231	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir330'>Mir330</a>
+Snord123	-1.85009039423829	2.46689582455698	-3.62068933774574	0.00273794187669866	0.012962621084287	-1.71578244093404	102	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord123'>Snord123</a>
+1700123M08Rik	-2.53907013725051	-0.265019789848831	-3.61128151512854	0.0027897908425338	0.0131535179807069	-1.57539508080877	14	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1700123M08Rik'>1700123M08Rik</a>
+U05342	2.83058680402627	0.79675702914225	3.60519476819122	0.00282386325723748	0.0132525688403876	-1.63602002228639	54	<a href='http://www.genecards.org/index.php?path=/Search/keyword/U05342'>U05342</a>
+Mir331	-1.23366463697674	4.50384654608554	-3.60339313514846	0.00283402874413198	0.0132525688403876	-2.05839651689923	359	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir331'>Mir331</a>
+Snord47	1.75254142711948	3.676071658915	3.56574123782182	0.00305512804060726	0.014228167731971	-1.9866272780716	277	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord47'>Snord47</a>
+1810026B05Rik	2.40748340219702	-0.486051677644913	3.55958270725964	0.00309291230781102	0.014345581069969	-1.66670102684768	15	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1810026B05Rik'>1810026B05Rik</a>
+Mir1933	-2.60309478178739	0.220871127749556	-3.55529124527092	0.00311951960536729	0.0144104124280327	-1.68059425943861	26	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1933'>Mir1933</a>
+Gm9899	-2.07308991765323	-0.941052160679803	-3.54532493149369	0.00318220422627889	0.0146407057346138	-1.68493975204853	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm9899'>Gm9899</a>
+Hspa13	2.27524541038784	-0.523818455835255	3.54060461550118	0.00321233452906321	0.0147199746894021	-1.69974419035356	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Hspa13'>Hspa13</a>
+Mir3096b	-1.20474634794453	4.70053095823646	-3.5153757202842	0.00337831126227612	0.0153571838655659	-2.25812559332021	435	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3096b'>Mir3096b</a>
+Snord93	-1.20474634794453	4.70053095823646	-3.5153757202842	0.00337831126227612	0.0153571838655659	-2.25812559332021	435	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord93'>Snord93</a>
+Adhfe1	2.52527478072387	0.179068747865736	3.50530102423767	0.00344697804598443	0.0156071505970962	-1.80634560509756	25	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Adhfe1'>Adhfe1</a>
+Gm10768	3.5358301921593	0.021906952859762	3.48225041539546	0.00360941220951063	0.0162780210713503	-1.87207612241023	59	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm10768'>Gm10768</a>
+Snord85	1.10352244207212	9.7813263715169	3.47953980186612	0.00362901230761682	0.0163019804842157	-2.72788678002978	15092	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord85'>Snord85</a>
+AF357399	1.79554087095325	2.33898958600026	3.47297259387192	0.00367694357668826	0.0164098488394083	-1.96818697726206	89	<a href='http://www.genecards.org/index.php?path=/Search/keyword/AF357399'>AF357399</a>
+Mir551b	2.15397612089142	-0.590132795422603	3.47231349486416	0.00368178904722922	0.0164098488394083	-1.82422890137775	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir551b'>Mir551b</a>
+Def8	2.41874321422316	-0.465993593620758	3.46859651584658	0.00370923535603452	0.0164678503550015	-1.83970905317218	16	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Def8'>Def8</a>
+Mir664	-1.01764634401405	5.37432688059702	-3.45211961435443	0.00383339754528852	0.0168755824717367	-2.46240607108039	632	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir664'>Mir664</a>
+Mir467c	2.31849317866793	0.658275206086465	3.45045370722881	0.00384618107849534	0.0168755824717367	-1.9100187677291	35	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir467c'>Mir467c</a>
+Mir345	-0.912671478268366	6.07047283018279	-3.44931934620133	0.00385491021641726	0.0168755824717367	-2.53238717399997	1042	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir345'>Mir345</a>
+Tysnd1	2.30243120612363	-0.498012096151827	3.44862877647117	0.0038602340272772	0.0168755824717367	-1.87482817968793	13	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Tysnd1'>Tysnd1</a>
+Szrd1	3.00773623992391	1.76282092941222	3.43919964294803	0.00393366880940514	0.0171175138601232	-1.97326991386	108	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Szrd1'>Szrd1</a>
+Snord35a	1.64122011441228	2.9111550248254	3.43698444459166	0.00395112336041969	0.0171175138601232	-2.13032503281622	131	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord35a'>Snord35a</a>
+Snora36b	-1.01237028448432	5.37669976851797	-3.43578817017266	0.00396058164686462	0.0171175138601232	-2.49502841436006	633	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora36b'>Snora36b</a>
+Mir3471-1	-1.1190522551011	4.8388269488082	-3.42504935436875	0.00404651146785495	0.017401703908276	-2.45454758690256	469	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3471-1'>Mir3471-1</a>
+Snord42b	1.04806162755878	6.10341205402338	3.42377413826923	0.00405683894794165	0.017401703908276	-2.57887542149696	1095	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord42b'>Snord42b</a>
+Snord23	2.9296105505117	1.31458313757935	3.40028372003562	0.00425187802628573	0.0181700105917304	-2.02991542506104	83	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord23'>Snord23</a>
+Wac	2.7504919030552	0.283618002868323	3.39632013594792	0.00428570220488658	0.0182462172230433	-2.02643747960115	36	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Wac'>Wac</a>
+Mir98	-0.933678340542421	7.94963852128455	-3.39430346367777	0.00430301532596754	0.0182518233714831	-2.78058118585178	4140	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir98'>Mir98</a>
+4930483K19Rik	2.52533407356931	-0.00211602021024845	3.38443072134124	0.00438878944604477	0.0185466991034707	-2.0252331979185	24	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930483K19Rik'>4930483K19Rik</a>
+9530036O11Rik	-2.18021083734	-0.880373807283523	-3.36944259471363	0.00452229090218708	0.0190403465660349	-2.01615459630653	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/9530036O11Rik'>9530036O11Rik</a>
+Airn	-3.32728005388875	1.05242623359369	-3.36289553627823	0.00458187540512432	0.0192202935192899	-2.09508526477381	66	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Airn'>Airn</a>
+Mir542	-1.22316159239699	3.81531438686763	-3.32742457590211	0.00491862125207608	0.0205573144638052	-2.50522353523098	225	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir542'>Mir542</a>
+Mir350	-1.56832295120394	3.2654986223895	-3.31591379494715	0.00503313311490562	0.0209591419128004	-2.43484812644587	172	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir350'>Mir350</a>
+Mir467d	-2.52245592103549	0.453062661337275	-3.31293337335217	0.00506321480472689	0.0210077385170668	-2.14396740548906	27	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir467d'>Mir467d</a>
+Gm10069	5.68607477678649	3.08099524867498	3.3046846231052	0.00514741011835455	0.0212796918298643	-2.27892670543982	1309	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm10069'>Gm10069</a>
+Wwp1	3.00070653341197	1.74135246228108	3.28733760371041	0.00532906211683886	0.0219415999009116	-2.26148023738523	118	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Wwp1'>Wwp1</a>
+Mir431	-2.52814898361935	0.729842447535775	-3.28575204794379	0.0053459813956647	0.0219415999009116	-2.20212311657876	36	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir431'>Mir431</a>
+1810058I24Rik	2.62271409770273	0.785774819657178	3.27879786751028	0.00542082417887067	0.0221690336490732	-2.25054020283081	50	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1810058I24Rik'>1810058I24Rik</a>
+Mir1950	2.90261468429164	1.12507136246027	3.27585207867393	0.00545284200159248	0.0222203311564894	-2.2663579061757	78	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1950'>Mir1950</a>
+1700045H11Rik	2.17220411664475	-0.157703843092941	3.2269553992009	0.00601270540485873	0.0244145795976648	-2.30225973272088	15	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1700045H11Rik'>1700045H11Rik</a>
+Mir3098	1.50327989079112	3.77759040172564	3.22488371497116	0.00603765136079478	0.0244289368888895	-2.67812879077923	259	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3098'>Mir3098</a>
+Mir92b	-1.33550563727296	3.82392790661174	-3.21643129376509	0.00614050279704137	0.0247572921958452	-2.71829841094789	237	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir92b'>Mir92b</a>
+Gm16157	2.66162389621631	-0.365224948706732	3.20356821793981	0.00630038071552899	0.0253124450578119	-2.34859094591427	22	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm16157'>Gm16157</a>
+Snord19	0.841113010089355	7.11055248976838	3.19415039125178	0.00642005717801694	0.0257027552284819	-3.11414489267883	2203	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord19'>Snord19</a>
+Schip1	-2.57567954952992	-0.153384190338395	-3.18549465102036	0.00653204236936578	0.0260045455633494	-2.38778174828683	17	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Schip1'>Schip1</a>
+Snord69	0.84304704580235	7.14897332827513	3.18307678347552	0.00656366958087888	0.0260045455633494	-3.13872359988574	2301	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord69'>Snord69</a>
+Mir3061	-1.52813229940924	2.87430787227175	-3.18306594661466	0.00656381167593746	0.0260045455633494	-2.63327753238114	119	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3061'>Mir3061</a>
+Mir29a	-0.877942320051101	11.0487374837586	-3.17676979444805	0.00664688724206556	0.0262425548207502	-3.41112827127731	33081	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir29a'>Mir29a</a>
+Gm10319	2.14644292502742	-0.590132795422603	3.17164218489659	0.00671531580422408	0.0264212942504127	-2.38832170685348	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm10319'>Gm10319</a>
+Mir127	-1.25650791022161	9.78648771687729	-3.16887488380797	0.00675253616433696	0.0264764390498573	-3.34593460449095	14429	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir127'>Mir127</a>
+B330016D10Rik	-1.92161264416092	-0.63693223477029	-3.1657281651115	0.0067951088367248	0.0264822665438203	-2.39563418410943	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/B330016D10Rik'>B330016D10Rik</a>
+Eci2	3.49526347553937	0.0311983516108461	3.16533536523053	0.00680044180310197	0.0264822665438203	-2.47536158350563	69	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Eci2'>Eci2</a>
+Mir128-2	-2.89379537629014	0.203236815749758	-3.14346309940017	0.00710405107482255	0.0275704839332399	-2.47229052342811	35	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir128-2'>Mir128-2</a>
+Snora65	1.80564358716833	2.25630817287283	3.13994836128033	0.00715407873897124	0.0276705214954786	-2.59842313949207	83	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora65'>Snora65</a>
+Snord38a	1.14948303605283	3.92210478649851	3.12106491021558	0.00742890451562957	0.0286364190957207	-2.90862714087175	255	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord38a'>Snord38a</a>
+Snord49b	1.06413907223879	6.40649794888962	3.10982427775322	0.0075974432295226	0.0291874839221727	-3.22360916919111	1485	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord49b'>Snord49b</a>
+G630025P09Rik	2.04699188377197	-0.244188556172649	3.10780445430196	0.00762812710513572	0.0292070235804022	-2.51605087870259	15	<a href='http://www.genecards.org/index.php?path=/Search/keyword/G630025P09Rik'>G630025P09Rik</a>
+Mir329	-2.25038749201629	0.143148280966294	-3.10219089596341	0.00771405119681339	0.0294372321590772	-2.52468319230879	18	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir329'>Mir329</a>
+Gm5105	-2.16408947287434	-0.894252721332116	-3.09357723434137	0.00784776462691287	0.029847664797692	-2.53204083131101	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5105'>Gm5105</a>
+1700001L05Rik	2.36321176153954	-0.504303555595595	3.08655241783997	0.00795851133538617	0.0301683104108825	-2.55344737484833	16	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1700001L05Rik'>1700001L05Rik</a>
+Snord2	0.691526499495304	8.00175923757187	3.08142494474571	0.008040321980135	0.030265949526277	-3.40026204758547	3954	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord2'>Snord2</a>
+Mir22	-0.847615802202714	16.7326675324719	-3.08005897908952	0.00806225653232276	0.030265949526277	-3.96615097802407	1751447	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir22'>Mir22</a>
+Mir22hg	-0.847524583315551	16.7327250619969	-3.07996011844832	0.00806384632426661	0.030265949526277	-3.96634849509949	1751491	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir22hg'>Mir22hg</a>
+1700012B15Rik	2.2557460290944	-0.13987829366259	3.07437268195085	0.00815420485488848	0.0305047466866484	-2.59032088872728	19	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1700012B15Rik'>1700012B15Rik</a>
+Mir185	-1.40702024721662	4.08694622913669	-3.05877067430607	0.008411855287644	0.0313657741281105	-3.06664608794292	331	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir185'>Mir185</a>
+Slc25a44	2.21491041672761	1.66497498687079	3.04421973608031	0.00865939699909311	0.032183622071548	-2.71149512021232	77	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Slc25a44'>Slc25a44</a>
+Mir495	-1.8776791373757	-0.650811148818883	-3.04203753845606	0.00869713645483206	0.0322189373213097	-2.62552265945633	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir495'>Mir495</a>
+Sec16b	3.05043595272399	0.157027195014887	3.02828873074633	0.00893867714364734	0.0330065715886784	-2.71905679017603	57	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Sec16b'>Sec16b</a>
+Mir152	-0.718432101776587	7.28616446583531	-3.01300789436766	0.00921491113521454	0.0339168180815477	-3.48441058966127	2398	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir152'>Mir152</a>
+Snora3	2.07140605143005	1.76186432056615	3.0107219189642	0.00925695325975535	0.0339620053677841	-2.78114890188917	69	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora3'>Snora3</a>
+2010003O02Rik	1.94956844186534	-0.0201000379109987	2.97528778647613	0.00993335310087066	0.0362443709129751	-2.76683258555442	17	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2010003O02Rik'>2010003O02Rik</a>
+Mir704	1.80973957230357	-0.756810762138252	2.9728569191809	0.00998150161417436	0.0362443709129751	-2.75225460174575	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir704'>Mir704</a>
+D130020L05Rik	2.51176492481985	1.19972413900365	2.97271570851407	0.00998430564726682	0.0362443709129751	-2.82735067383733	52	<a href='http://www.genecards.org/index.php?path=/Search/keyword/D130020L05Rik'>D130020L05Rik</a>
+Mir3076	-2.06400546664394	-0.027699510367659	-2.97161874120075	0.0100061146692262	0.0362443709129751	-2.75226107651724	17	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3076'>Mir3076</a>
+Mirlet7c-1	-0.837889959835657	5.12475158025001	-2.96511158812865	0.0101364526370322	0.0366002925913093	-3.39152169935695	536	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mirlet7c-1'>Mirlet7c-1</a>
+Mir540	-2.19546334412823	0.490670971257216	-2.96107695486126	0.0102181042879641	0.0367787286831769	-2.78918578498352	25	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir540'>Mir540</a>
+Mir1947	-1.28776936588478	3.27191581050928	-2.95683139992983	0.0103047236916254	0.0369738670822157	-3.13442994008256	146	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1947'>Mir1947</a>
+9130019P16Rik	2.19950155178161	0.0491090861538386	2.93627487051494	0.0107344511680762	0.0383950118582288	-2.85952778968786	20	<a href='http://www.genecards.org/index.php?path=/Search/keyword/9130019P16Rik'>9130019P16Rik</a>
+Mir5121	1.92484055344077	0.963995516493567	2.91681375354519	0.0111574945019998	0.0397834413336931	-2.90528656811773	37	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir5121'>Mir5121</a>
+B430319G15Rik	-1.98479980231837	-0.986373420602892	-2.90027155266244	0.0115299314828684	0.0408786538511516	-2.88966321680022	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/B430319G15Rik'>B430319G15Rik</a>
+Mir351	-0.833417329407842	8.58289887759314	-2.89999295816495	0.0115363072217974	0.0408786538511516	-3.79447142137588	5692	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir351'>Mir351</a>
+D330050I16Rik	1.78527438588565	-0.392012482832458	2.89505348884379	0.0116499250396066	0.0411534503721088	-2.89805092182303	11	<a href='http://www.genecards.org/index.php?path=/Search/keyword/D330050I16Rik'>D330050I16Rik</a>
+BC024386	2.76807972012068	-0.350592172752806	2.88853915590151	0.0118014481853742	0.0415600382083702	-2.93769383343029	35	<a href='http://www.genecards.org/index.php?path=/Search/keyword/BC024386'>BC024386</a>
+Mir666	-2.07579086945099	-0.498012096151827	-2.87668024285998	0.0120822641583993	0.0424180412453341	-2.935960499869	9	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir666'>Mir666</a>
+Mir19a	1.09579604803789	3.73141492889975	2.86437745877971	0.0123805124227085	0.0433317934794797	-3.37709843179263	223	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir19a'>Mir19a</a>
+Numb	1.68732685590953	2.04652538144382	2.86121813573409	0.0124582585716259	0.0434705597254591	-3.09454193475081	80	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Numb'>Numb</a>
+Mir743b	1.75236219547595	-0.788253108012747	2.85924586889851	0.0125070353152586	0.043507705166799	-2.96109586080316	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir743b'>Mir743b</a>
+Mir466f-3	2.69172899990669	1.87893214035262	2.85764483454932	0.012546768496086	0.0435132609545109	-3.07809643101419	134	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir466f-3'>Mir466f-3</a>
+Snora64	2.4307644292688	0.761833001151837	2.85484959589604	0.0126164349935154	0.0435532556947262	-3.03394915069077	47	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora64'>Snora64</a>
+Trmt61b	2.31260437934785	-0.537538901613448	2.85283128922496	0.0126669731509781	0.0435532556947262	-2.98304494636545	18	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Trmt61b'>Trmt61b</a>
+C130080G10Rik	-1.86190650840199	-1.04705177399917	-2.85259853175366	0.0126728141022341	0.0435532556947262	-2.97869388313859	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/C130080G10Rik'>C130080G10Rik</a>
+Mir146	-0.747535639173072	9.8698371568429	-2.82836188364647	0.0132956711142425	0.045554137729091	-4.01615829841473	13917	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir146'>Mir146</a>
+Mir449a	-1.79604146328396	-1.07849411987367	-2.8268741085019	0.0133348659084281	0.045554137729091	-3.02729704133418	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir449a'>Mir449a</a>
+Ncaph2	2.43172128495717	0.531053368370468	2.81514840260429	0.0136477529969634	0.0464838393120456	-3.10990472720523	39	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Ncaph2'>Ncaph2</a>
+Tmem41a	2.13366400352273	-0.61462282166951	2.81019216927593	0.0137821511685655	0.0468018883432536	-3.05559526679725	14	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Tmem41a'>Tmem41a</a>
+Mir337	-2.00512882554678	1.46245475734951	-2.790176090596	0.0143381997019222	0.0484912300051582	-3.15685281038144	50	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir337'>Mir337</a>
+E430016F16Rik	-1.97871005920294	-0.986373420602892	-2.78924386549867	0.0143646237876805	0.0484912300051582	-3.09307014868296	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/E430016F16Rik'>E430016F16Rik</a>
+1700003F17Rik	-2.01422348895548	0.00986412853889808	-2.78534021594328	0.0144757903878217	0.0487223505383617	-3.09728477834654	16	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1700003F17Rik'>1700003F17Rik</a>
+5730522E02Rik	1.77943144260577	-0.402623595030772	2.78153548351825	0.0145849474469889	0.0489453677559245	-3.10514832323792	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/5730522E02Rik'>5730522E02Rik</a>
+Snord32a	0.731701165103898	7.36041411624865	2.77936808794083	0.0146474880967064	0.0490110965347272	-3.93874361373315	2646	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord32a'>Snord32a</a>
+Ccl25	1.82691173511948	-0.742931848089659	2.76634551467819	0.0150287990280197	0.0501399406168728	-3.13119236947949	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Ccl25'>Ccl25</a>
+Bc1	1.4447966027473	5.60396756501899	2.76417137258444	0.015093394998458	0.0502086405050747	-3.80973281446833	1034	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Bc1'>Bc1</a>
+Mir92-2	0.841738777296982	7.67150490176917	2.75570725400377	0.015347458592434	0.0509053786452535	-4.00630959541651	3238	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir92-2'>Mir92-2</a>
+Gm16023	2.83755782890821	0.231660734523689	2.74997768567304	0.0155217992534112	0.051334414342441	-3.23123254571433	61	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm16023'>Gm16023</a>
+Mir463	1.7496368661484	-0.788253108012747	2.74746508869923	0.0155988599062727	0.051440170962593	-3.16503205634054	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir463'>Mir463</a>
+1810008I18Rik	2.42034344843247	-0.486051677644913	2.74392263242908	0.0157081389909388	0.0516512581805798	-3.18685172400794	25	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1810008I18Rik'>1810008I18Rik</a>
+Gm16119	2.15928464558089	0.141491903029062	2.7402336372813	0.0158227303686605	0.0517925809899256	-3.22270297555294	24	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm16119'>Gm16119</a>
+2010308F09Rik	-1.83277349898908	-0.650811148818883	-2.73961897562678	0.0158419025113795	0.0517925809899256	-3.18111223859539	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2010308F09Rik'>2010308F09Rik</a>
+Gm8883	2.16409799450603	-0.590132795422603	2.72505563686563	0.0163028203034417	0.0529872269292577	-3.21224705829732	16	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm8883'>Gm8883</a>
+Zfp862	2.16409799450603	-0.590132795422603	2.72505563686563	0.0163028203034417	0.0529872269292577	-3.21224705829732	16	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Zfp862'>Zfp862</a>
+Snhg7	1.72599658448324	2.92713305382255	2.72369233450925	0.0163466291666071	0.0529872269292577	-3.48946421579912	173	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snhg7'>Snhg7</a>
+B830017H08Rik	-2.23343112594958	-0.833574367935836	-2.72209538930301	0.016398091528245	0.0530034629850638	-3.21732724703038	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/B830017H08Rik'>B830017H08Rik</a>
+1810064F22Rik	2.10429563053184	-0.628239618113655	2.71233407077621	0.0167160942777747	0.0537469782312529	-3.23263196069571	14	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1810064F22Rik'>1810064F22Rik</a>
+Mir297c	-2.59766718982369	-0.523818455835255	-2.71214450340864	0.0167223288975414	0.0537469782312529	-3.25125579861584	16	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir297c'>Mir297c</a>
+Mir3065	-1.15841548117293	4.89782194523564	-2.69932982501886	0.0171490634567944	0.0546270939470388	-3.86797461891443	469	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3065'>Mir3065</a>
+Mir338	-1.15841548117293	4.89782194523564	-2.69932982501886	0.0171490634567944	0.0546270939470388	-3.86797461891443	469	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir338'>Mir338</a>
+Snord12	0.862355865323009	7.21183801132978	2.69866680699734	0.017171427527834	0.0546270939470388	-4.08039835847175	2566	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord12'>Snord12</a>
+Gm16551	1.95751791415313	-0.691386427467094	2.69401162790859	0.0173292489773132	0.0546270939470388	-3.26351851959596	11	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm16551'>Gm16551</a>
+Mir1938	-1.6694250746775	-1.13917247326995	-2.69395153729379	0.0173312953626889	0.0546270939470388	-3.27380411394135	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1938'>Mir1938</a>
+Mir384	-1.6694250746775	-1.13917247326995	-2.69395153729379	0.0173312953626889	0.0546270939470388	-3.27380411394135	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir384'>Mir384</a>
+Sec14l1	-1.6694250746775	-1.13917247326995	-2.69395153729379	0.0173312953626889	0.0546270939470388	-3.27380411394135	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Sec14l1'>Sec14l1</a>
+A530013C23Rik	2.10076433042777	-0.628239618113655	2.67776214138051	0.0178912486859939	0.056236679754047	-3.29508901202161	14	<a href='http://www.genecards.org/index.php?path=/Search/keyword/A530013C23Rik'>A530013C23Rik</a>
+Gm9920	1.6285204207954	-0.848931461409027	2.67099225409632	0.0181305686626977	0.0566766543675016	-3.30261681920118	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm9920'>Gm9920</a>
+Mir3096	1.6285204207954	-0.848931461409027	2.67099225409632	0.0181305686626977	0.0566766543675016	-3.30261681920118	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3096'>Mir3096</a>
+Runx2	-2.05940172171601	0.19321552216426	-2.66798439607752	0.0182378909516821	0.0568298554460666	-3.31709929184916	18	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Runx2'>Runx2</a>
+Mir1199	-1.80452318263558	-0.286012869513089	-2.66623221676357	0.0183006932250553	0.0568298554460666	-3.30697738722689	11	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1199'>Mir1199</a>
+2810013P06Rik	1.73280899888147	-0.254570523638594	2.66544441649986	0.0183289980755061	0.0568298554460666	-3.31814833648003	13	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2810013P06Rik'>2810013P06Rik</a>
+Mir139	-0.71676951546528	5.60987527682552	-2.6551603087927	0.0187024067912338	0.0578304773680157	-4.03578216454232	751	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir139'>Mir139</a>
+Syce2	2.36455525863438	-0.504303555595595	2.65072370278831	0.0188657609520281	0.0581779276926056	-3.35376683182341	26	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Syce2'>Syce2</a>
+Hsf4	1.75853048276747	-0.027699510367659	2.63272367541842	0.0195427890611213	0.060103294659675	-3.38335065718976	17	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Hsf4'>Hsf4</a>
+9530026P05Rik	-2.07695780402641	0.308348068257344	-2.63023447836339	0.0196382434958373	0.0602345049159956	-3.38900744489907	20	<a href='http://www.genecards.org/index.php?path=/Search/keyword/9530026P05Rik'>9530026P05Rik</a>
+F730035M05Rik	1.78278284441709	0.0460524556882713	2.60073804597223	0.0208042043193282	0.0636396705853981	-3.45006336955945	17	<a href='http://www.genecards.org/index.php?path=/Search/keyword/F730035M05Rik'>F730035M05Rik</a>
+4931440P22Rik	1.81357503948527	-0.34669122290937	2.59692706678062	0.0209596355730796	0.0639437010397962	-3.44244562957201	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4931440P22Rik'>4931440P22Rik</a>
+Mir300	-1.68375330243594	3.41000156536173	-2.5819475209075	0.0215814969001033	0.0656653012347144	-3.85223959755949	222	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir300'>Mir300</a>
+Gm9961	1.6141478502722	-0.484133182103234	2.57010065554055	0.0220858578259184	0.0668716722449952	-3.48214581462349	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm9961'>Gm9961</a>
+2900060B14Rik	-1.19518787351076	3.46457469939205	-2.56923876538494	0.0221229909127292	0.0668716722449952	-3.89704508052604	185	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2900060B14Rik'>2900060B14Rik</a>
+Mir411	-1.00605950591069	6.99892994877789	-2.56852458872886	0.0221538055290168	0.0668716722449952	-4.310335894974	2196	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir411'>Mir411</a>
+Mir673	-1.3090170207406	1.82295295242957	-2.56480697753964	0.0223148777778054	0.0671801465553455	-3.62107180274171	51	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir673'>Mir673</a>
+Gm5088	-1.68701668543175	-1.13917247326995	-2.55941235619776	0.0225506148115993	0.0677111881579862	-3.51525248418991	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5088'>Gm5088</a>
+Tor2a	2.07995668744553	-0.61904848868591	2.55252291882178	0.0228551574897157	0.0684454978891487	-3.51995132920037	16	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Tor2a'>Tor2a</a>
+Mir1929	-1.69214227634269	-1.13917247326995	-2.5510179798629	0.0229222065165283	0.0684665906684784	-3.53018502209241	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1929'>Mir1929</a>
+Gm12295	-1.69666721026032	-1.13917247326995	-2.54771186173241	0.0230701674123488	0.0687286188446215	-3.53606163444577	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm12295'>Gm12295</a>
+Wdr13	-1.72526707110706	-0.147092730894626	-2.53924168587016	0.0234534382441355	0.0696884714493714	-3.52799276824936	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Wdr13'>Wdr13</a>
+St7l	1.62230300798708	0.897522708635819	2.52666370286734	0.0240338880626592	0.0712277046220627	-3.60118587779941	32	<a href='http://www.genecards.org/index.php?path=/Search/keyword/St7l'>St7l</a>
+Snord88c	0.793290174312999	4.47693446317466	2.50505317099491	0.0250634970146661	0.0740866582739222	-4.17079027962479	341	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord88c'>Snord88c</a>
+9330175M20Rik	-1.65022439160042	-0.360570136957963	-2.50294066783667	0.0251663831454311	0.0741985611600436	-3.59490203212403	9	<a href='http://www.genecards.org/index.php?path=/Search/keyword/9330175M20Rik'>9330175M20Rik</a>
+Snora52	1.11047151370588	2.69319347264049	2.50050576985066	0.0252854729408082	0.0742992649502222	-3.88083546486857	105	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora52'>Snora52</a>
+4933405D12Rik	2.28373557503359	-0.125999379613997	2.49952793100309	0.0253334503629621	0.0742992649502222	-3.64207314883416	26	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4933405D12Rik'>4933405D12Rik</a>
+Mir188	-1.84047092737597	1.30222680574037	-2.49825793655251	0.0253958924895589	0.0742992649502222	-3.67062190136747	41	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir188'>Mir188</a>
+Mir205	1.92476770177287	-0.714181147408868	2.49436665703146	0.0255881349007889	0.0746702350941181	-3.61910043615221	13	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir205'>Mir205</a>
+Mir29b-2	-1.76343390631061	1.19462262736195	-2.491486533954	0.0257313191461785	0.0747071028176607	-3.66952491758492	41	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir29b-2'>Mir29b-2</a>
+Snord100	0.630343774928686	6.02538660524635	2.49147851197563	0.0257317190248384	0.0747071028176607	-4.3727044437044	1006	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord100'>Snord100</a>
+Mir103-1	1.66401353804538	-0.178535076769122	2.48869237583317	0.0258709623692558	0.0749123841663655	-3.63209662533681	14	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir103-1'>Mir103-1</a>
+Snord67	1.44797500570103	2.44125660341038	2.48744103910754	0.0259337350970328	0.0749123841663655	-3.84438090974652	108	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord67'>Snord67</a>
+Mir378b	-1.87217458287095	-1.04230579272429	-2.48543799390718	0.0260345203956202	0.07501360548334	-3.63953394774132	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378b'>Mir378b</a>
+Stap2	1.82543646576299	0.360783493796099	2.47215410233116	0.0267124555123547	0.0766751025232241	-3.68285167340431	25	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Stap2'>Stap2</a>
+Abhd1	1.9251911184693	-0.706743520940286	2.47151360035917	0.0267455659984603	0.0766751025232241	-3.65951891456996	13	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Abhd1'>Abhd1</a>
+Crebzf	2.18345173240976	1.01056858325673	2.46941691788336	0.0268542277090025	0.0766788467965674	-3.72491986207361	48	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Crebzf'>Crebzf</a>
+AW495222	3.12693001673928	0.217900170575655	2.46889622052332	0.0268812784562901	0.0766788467965674	-3.7522647303971	101	<a href='http://www.genecards.org/index.php?path=/Search/keyword/AW495222'>AW495222</a>
+Lrrc28	2.42525008262091	0.708273211214943	2.46119616740811	0.0272843555867779	0.077634537966368	-3.75212597460025	60	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Lrrc28'>Lrrc28</a>
+Mir3086	-1.56502610075238	0.163979514642475	-2.45070863513763	0.0278426426188866	0.079026008030223	-3.67658416235536	15	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3086'>Mir3086</a>
+Gm16548	1.56554530187766	-0.880373807283523	2.43719245534725	0.028578244472197	0.0809125978728953	-3.7171315266521	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm16548'>Gm16548</a>
+Vsig8	0.720909981822672	5.46827442991139	2.4297652846464	0.0289903098093856	0.081876097753735	-4.42992368125479	711	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Vsig8'>Vsig8</a>
+Mllt10	1.64313940342435	2.00106077397987	2.42643449288836	0.0291769377903763	0.0821624443172407	-3.88522168534726	76	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mllt10'>Mllt10</a>
+Snord37	0.718235154642642	5.26607014192141	2.42421441307507	0.0293019662978149	0.0821624443172407	-4.41840621005442	605	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord37'>Snord37</a>
+2310044G17Rik	1.83521282323275	0.25478388047673	2.42411236612262	0.0293077255364741	0.0821624443172407	-3.77290246486377	21	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2310044G17Rik'>2310044G17Rik</a>
+Mir5109	1.91674990639075	5.26141207092908	2.4205606649453	0.0295088463344336	0.0825235138911489	-4.39344655492679	1282	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir5109'>Mir5109</a>
+1700028E10Rik	1.54839823984953	-0.345213043484771	2.41736388881311	0.0296909918731214	0.0828298819736711	-3.7511992998099	11	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1700028E10Rik'>1700028E10Rik</a>
+Mea1	1.54661886587012	-0.101771470971538	2.4138331460667	0.0298934095831866	0.0831911715473558	-3.76260805956638	13	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mea1'>Mea1</a>
+Snora74a	-1.73489546483347	1.01966577101052	-2.40803895916142	0.0302284388032876	0.0839188532227522	-3.80206412811815	36	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora74a'>Snora74a</a>
+Mir191	-0.655767170712639	13.5617906330993	-2.39884764518688	0.0307672305375651	0.0851401619055862	-5.06132700567092	174890	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir191'>Mir191</a>
+Mir1949	-1.81819327722704	-1.07849411987367	-2.39799614454486	0.0308176046161324	0.0851401619055862	-3.79424293296871	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1949'>Mir1949</a>
+Mir1198	1.58891563084634	1.17557415725746	2.39059542110177	0.0312587378593833	0.086150289607624	-3.8609699445768	43	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1198'>Mir1198</a>
+Cldn25	1.85104613563129	-0.734239231433024	2.38535835022853	0.0315745192814028	0.0868109072291099	-3.80901008552036	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Cldn25'>Cldn25</a>
+3110045C21Rik	1.65443039841412	0.203826634362574	2.38155453756473	0.0318057752099395	0.0872365132561082	-3.82495974541955	21	<a href='http://www.genecards.org/index.php?path=/Search/keyword/3110045C21Rik'>3110045C21Rik</a>
+A330009N23Rik	-1.65876461460145	-1.13917247326995	-2.36252069958505	0.0329872919163081	0.0902246398210002	-3.86075992930999	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/A330009N23Rik'>A330009N23Rik</a>
+4930412C18Rik	-1.71539919467515	-1.13917247326995	-2.36022700442918	0.0331324488036802	0.0902246398210002	-3.86472183787187	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930412C18Rik'>4930412C18Rik</a>
+Gm17769	-1.71539919467515	-1.13917247326995	-2.36022700442918	0.0331324488036802	0.0902246398210002	-3.86472183787187	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm17769'>Gm17769</a>
+Fth1	2.86103494155137	3.45595627169968	2.35821583980086	0.033260223411433	0.0903569402677262	-4.19586341531867	625	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Fth1'>Fth1</a>
+4833417C18Rik	1.47974694653215	-0.544811535499514	2.35068477635695	0.0337428496416542	0.0914503359646734	-3.86474671238307	9	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4833417C18Rik'>4833417C18Rik</a>
+Snora61	0.958904821800182	3.29767563160608	2.349125503029	0.0338436003101147	0.0915060378053102	-4.26190631619714	164	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora61'>Snora61</a>
+Mirlet7f-2	0.650708366569944	9.71888537299185	2.34186730999564	0.0343163384594052	0.0925648751351804	-4.91362837250212	14033	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mirlet7f-2'>Mirlet7f-2</a>
+Mir484	-0.729527631490827	7.08906245513894	-2.3224356166388	0.0356128817086712	0.095835608560363	-4.76719481541216	2052	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir484'>Mir484</a>
+A630066F11Rik	1.44515529589515	-0.941052160679803	2.31716732167662	0.0359722924599672	0.0963708221549233	-3.92438209949561	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/A630066F11Rik'>A630066F11Rik</a>
+A730017L22Rik	2.05481659238372	-0.239213430165402	2.31696857375682	0.0359859181283499	0.0963708221549233	-3.9446476842384	21	<a href='http://www.genecards.org/index.php?path=/Search/keyword/A730017L22Rik'>A730017L22Rik</a>
+Ankrd10	1.8458518819756	-0.032400500918623	2.31581421766513	0.0360651543033762	0.0963708221549233	-3.94922969635093	18	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Ankrd10'>Ankrd10</a>
+9330179D12Rik	-1.85045093530144	1.28320177813767	-2.31096269706071	0.0363999711565358	0.0970382408635685	-3.9951686511153	40	<a href='http://www.genecards.org/index.php?path=/Search/keyword/9330179D12Rik'>9330179D12Rik</a>
+Snora62	1.7847261774294	-0.244188556172649	2.29775908931167	0.0373260968205211	0.0992752365319687	-3.96525604386916	17	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora62'>Snora62</a>
+BC024582	1.59980554588654	-0.452690836228738	2.2959268866433	0.0374563520512198	0.0993899946289343	-3.96118314063755	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/BC024582'>BC024582</a>
+Gm10804	1.52979741848186	-0.355824155683085	2.29375082460336	0.0376116093012649	0.0994728784445405	-3.96360070348265	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm10804'>Gm10804</a>
+Mir1195	1.10164801174588	3.09590694872149	2.29304709119496	0.0376619487187042	0.0994728784445405	-4.32472042528613	144	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1195'>Mir1195</a>
+Gorasp2	1.73210701934952	0.154556788162208	2.28600861467189	0.03816892734941	0.100579090313341	-3.99587343487878	24	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gorasp2'>Gorasp2</a>
+5730420D15Rik	1.62853621883357	-0.848931461409027	2.27860458389794	0.0387091654979492	0.101767644776867	-3.99077412899541	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/5730420D15Rik'>5730420D15Rik</a>
+Mirlet7f-1	-0.614882576643158	5.68980618928649	-2.27248837673306	0.0391608536660756	0.102718469041361	-4.74250560785076	779	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mirlet7f-1'>Mirlet7f-1</a>
+0610009L18Rik	-1.61889807816313	0.265553460945444	-2.26526136567524	0.0397009617671157	0.103777261528111	-3.99536063610116	21	<a href='http://www.genecards.org/index.php?path=/Search/keyword/0610009L18Rik'>0610009L18Rik</a>
+Snhg3	1.25378785890833	2.38956644178022	2.26464378812804	0.0397474393896485	0.103777261528111	-4.23895965644335	94	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snhg3'>Snhg3</a>
+Mir297-2	1.46684984163613	1.40872493183085	2.26345073111919	0.0398373712088629	0.103777261528111	-4.09858373085422	47	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir297-2'>Mir297-2</a>
+Etfb	2.40847795385732	0.265851908477543	2.26169079632117	0.0399703828812269	0.103886576007927	-4.07904638296427	53	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Etfb'>Etfb</a>
+Mir708	-1.85451172422601	-0.280376883322022	-2.25778324055568	0.0402671991288784	0.104420168650114	-4.0216739515904	16	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir708'>Mir708</a>
+Rchy1	1.62884124887726	-0.438811922180145	2.25361813300649	0.0405858566094605	0.105007851227652	-4.03354975134699	11	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Rchy1'>Rchy1</a>
+A730056A06Rik	-1.68694694851363	-1.13917247326995	-2.24683042206407	0.0411102355769964	0.105912931059682	-4.05854864097368	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/A730056A06Rik'>A730056A06Rik</a>
+4933406I18Rik	1.77699338800155	-0.768738207773087	2.24668779416224	0.0411213220503411	0.105912931059682	-4.04580334564085	11	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4933406I18Rik'>4933406I18Rik</a>
+Mir134	-1.97599424729025	0.963837048223167	-2.23531953342299	0.0420140490275288	0.107968535901825	-4.10273890592774	40	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir134'>Mir134</a>
+0610040F04Rik	1.48024531718237	-0.126261497218445	2.21863530367332	0.0433571530862421	0.111169689149219	-4.09406770500723	13	<a href='http://www.genecards.org/index.php?path=/Search/keyword/0610040F04Rik'>0610040F04Rik</a>
+Hyi	1.7208723887239	-0.798864220211061	2.21727225982332	0.0434686369972673	0.111205638596148	-4.09496822692958	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Hyi'>Hyi</a>
+Mir19b-2	1.46199574456486	-0.157703843092941	2.21491518136265	0.0436620562951831	0.111450573227749	-4.09725345928943	13	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir19b-2'>Mir19b-2</a>
+Dnajc5	1.72175747703832	0.127791187493102	2.20641034213855	0.0443666638363991	0.112996346958329	-4.1264696449174	24	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnajc5'>Dnajc5</a>
+A330023F24Rik	-0.702900153988052	8.59775002327938	-2.19591230206849	0.0452510530552774	0.114819027522333	-5.09936581845105	6103	<a href='http://www.genecards.org/index.php?path=/Search/keyword/A330023F24Rik'>A330023F24Rik</a>
+Mir5117	-0.936491371721633	3.3130102793186	-2.19552988269139	0.0452835779010078	0.114819027522333	-4.54124266085371	153	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir5117'>Mir5117</a>
+Mir376a	-1.47455098239027	-0.835052547360434	-2.1925218271152	0.0455401753877667	0.11521361445109	-4.13790833966528	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir376a'>Mir376a</a>
+C530005A16Rik	1.59621643209164	-0.0517042297735718	2.19129548146478	0.0456451756588884	0.115223773068123	-4.14802186280035	15	<a href='http://www.genecards.org/index.php?path=/Search/keyword/C530005A16Rik'>C530005A16Rik</a>
+Mir29c	-0.711325240372844	8.57976498765981	-2.18303555556971	0.0463582979168776	0.116551708876032	-5.12055952980097	6038	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir29c'>Mir29c</a>
+Snora17	1.61038572109377	2.63473165643875	2.18283746936672	0.046375526581699	0.116551708876032	-4.41075432236771	155	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora17'>Snora17</a>
+Gm12992	1.67719387198237	-0.452690836228738	2.17669534214676	0.04691271219153	0.117642647495683	-4.16199311590905	14	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm12992'>Gm12992</a>
+4933425B07Rik	1.566045114104	-0.880373807283523	2.1731277221669	0.0472273890461801	0.118135825145526	-4.16761720498767	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4933425B07Rik'>4933425B07Rik</a>
+4932412D23Rik	-1.44767473084559	-1.24517208658932	-2.17095503836684	0.0474199894098607	0.118135825145526	-4.19574836919915	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4932412D23Rik'>4932412D23Rik</a>
+Smpx	-1.44767473084559	-1.24517208658932	-2.17095503836684	0.0474199894098607	0.118135825145526	-4.19574836919915	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Smpx'>Smpx</a>
+Gm16833	1.43772363562533	0.00422814234783093	2.16359562114833	0.0480778206167906	0.119513710945007	-4.18236836922897	15	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm16833'>Gm16833</a>
+Mir3089	-1.46210970943343	-1.24517208658932	-2.15543507336627	0.0488171825310707	0.120734101973115	-4.22155997764311	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3089'>Mir3089</a>
+Snora7a	1.7230694099937	1.73375263955762	2.15504822558148	0.048852492789084	0.120734101973115	-4.31592015811305	80	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora7a'>Snora7a</a>
+2310015A10Rik	1.51712536676038	-0.90486383353043	2.15439473012054	0.0489121957425213	0.120734101973115	-4.19854386809234	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2310015A10Rik'>2310015A10Rik</a>
+AW112010	1.99789847267928	0.0701015602482627	2.15352220222733	0.0489920150863736	0.120734101973115	-4.22796047652863	34	<a href='http://www.genecards.org/index.php?path=/Search/keyword/AW112010'>AW112010</a>
+Pglyrp2	2.13000407982332	-0.625897547790957	2.1382953912996	0.050404600122275	0.123947518835163	-4.23118827095858	27	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Pglyrp2'>Pglyrp2</a>
+R74862	1.46156334047426	0.026537555448611	2.13628776933242	0.0505936418662866	0.124144828751469	-4.22999882095606	15	<a href='http://www.genecards.org/index.php?path=/Search/keyword/R74862'>R74862</a>
+Snora28	1.12037820753744	2.12526039705926	2.12930512434667	0.0512562751008916	0.125500879592526	-4.42817337501701	71	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora28'>Snora28</a>
+Cd40	-1.37088395935442	-1.27661443246381	-2.12752810799839	0.0514261885899383	0.125647283043083	-4.27058401928142	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Cd40'>Cd40</a>
+Mug-ps1	2.13180518001054	-0.635454055345691	2.12264061264248	0.0518962135703567	0.126524742914053	-4.25630236233275	31	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mug-ps1'>Mug-ps1</a>
+A630072M18Rik	1.38270587147115	0.396971820945472	2.11893446805287	0.0522552789377958	0.127117232913158	-4.26481829202589	20	<a href='http://www.genecards.org/index.php?path=/Search/keyword/A630072M18Rik'>A630072M18Rik</a>
+9430083A17Rik	1.47463750425962	-0.925695067206612	2.11783696007545	0.0523620503673834	0.127117232913158	-4.25875097666518	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/9430083A17Rik'>9430083A17Rik</a>
+Mir1934	-1.57424505068045	-0.635454055345691	-2.11625143263769	0.0525166556449856	0.127221877050804	-4.25830313630768	9	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1934'>Mir1934</a>
+Snhg4	-1.12748951163344	1.68874582221391	-2.10271220257256	0.0538541790241838	0.130185631920749	-4.40346908432753	47	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snhg4'>Snhg4</a>
+Mir669e	1.4372851263053	-0.148570910319225	2.09754754034625	0.0543726361448265	0.131161052518493	-4.29239386401532	13	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir669e'>Mir669e</a>
+9430008C03Rik	1.75693578729127	0.363840124261666	2.09398906309311	0.054732534541466	0.131750679138845	-4.32757583432609	26	<a href='http://www.genecards.org/index.php?path=/Search/keyword/9430008C03Rik'>9430008C03Rik</a>
+C030037D09Rik	1.44249836924774	-0.941052160679803	2.08964460798292	0.0551749074500188	0.132204324416187	-4.30482301369224	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/C030037D09Rik'>C030037D09Rik</a>
+Wdr73	1.44249836924774	-0.941052160679803	2.08964460798292	0.0551749074500188	0.132204324416187	-4.30482301369224	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Wdr73'>Wdr73</a>
+A230108P19Rik	1.49352479961928	0.250614055858426	2.08783829894219	0.0553598038831607	0.132204324416187	-4.31611624705347	21	<a href='http://www.genecards.org/index.php?path=/Search/keyword/A230108P19Rik'>A230108P19Rik</a>
+B230206H07Rik	1.44241701736279	-0.941052160679803	2.08759786205388	0.0553844584320223	0.132204324416187	-4.3081590960531	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/B230206H07Rik'>B230206H07Rik</a>
+Snord55	0.601021636432394	6.97866331241363	2.08546096371218	0.0556040229210925	0.132208091094402	-5.17041448286456	2070	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord55'>Snord55</a>
+Ralgps2	1.88483656314977	0.227262055965901	2.08532736079326	0.0556177771475135	0.132208091094402	-4.34269584383277	30	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Ralgps2'>Ralgps2</a>
+Mir33	0.994045785258037	2.79490734914157	2.08206634259786	0.055954469010935	0.132731910897041	-4.63235497043256	118	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir33'>Mir33</a>
+Mir26a-1	-0.807612985022876	4.30478785875254	-2.07928199044436	0.0562434329588863	0.13314057470143	-4.90515725875701	302	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir26a-1'>Mir26a-1</a>
+Gm16845	1.58909272532801	0.693110936601907	2.07661019420121	0.0565220086427535	0.133523005924186	-4.35651524620671	30	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm16845'>Gm16845</a>
+Gm15417	1.5342975077552	0.98095079124996	2.07236996254055	0.0569667294167582	0.134295533604382	-4.38415298913751	35	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm15417'>Gm15417</a>
+Tmem161b	1.62214843774913	-0.848931461409027	2.06567840236373	0.0576751098770028	0.135602143587659	-4.3444683065412	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Tmem161b'>Tmem161b</a>
+0610039K10Rik	1.59784774087558	0.19965680974427	2.0648940719261	0.0577586693984243	0.135602143587659	-4.35652602439924	21	<a href='http://www.genecards.org/index.php?path=/Search/keyword/0610039K10Rik'>0610039K10Rik</a>
+E230016K23Rik	-1.72852657300674	-1.13917247326995	-2.05875394572702	0.0584166748798269	0.136730583937275	-4.37016708474507	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/E230016K23Rik'>E230016K23Rik</a>
+2900056M20Rik	-1.65506739394547	-0.558690449548107	-2.05452050389929	0.0588743595154887	0.136730583937275	-4.36084200194152	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2900056M20Rik'>2900056M20Rik</a>
+Mir671	0.562605162336286	5.98852427457086	2.05429817680062	0.0588984865622872	0.136730583937275	-5.14108074312137	973	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir671'>Mir671</a>
+4931408D14Rik	1.96514847475323	-0.696132408741971	2.05392305419837	0.0589392156613288	0.136730583937275	-4.36610698383729	22	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4931408D14Rik'>4931408D14Rik</a>
+Gm16998	1.69004828050554	0.625421285257375	2.05268667282661	0.0590736396779562	0.136730583937275	-4.40968404758219	28	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm16998'>Gm16998</a>
+Gm16880	1.44362454501385	-0.941052160679803	2.05264516314336	0.0590781576521265	0.136730583937275	-4.36487132437809	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm16880'>Gm16880</a>
+Gm20605	1.44362454501385	-0.941052160679803	2.05264516314336	0.0590781576521265	0.136730583937275	-4.36487132437809	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm20605'>Gm20605</a>
+Angel2	2.00212254672889	-0.0888847843510248	2.04370859875966	0.0600582524306836	0.13871754255751	-4.40649208108809	28	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Angel2'>Angel2</a>
+Mir3082	-0.840503124788145	2.98078155227528	-2.04091866162716	0.0603672767363008	0.139149621729534	-4.74512204880153	112	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3082'>Mir3082</a>
+4930556M19Rik	1.91670992783053	-0.130687164234845	2.03879415031149	0.0606035740806922	0.139412657310624	-4.40877400780406	23	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930556M19Rik'>4930556M19Rik</a>
+Rian	-1.1485219400328	2.35394460295566	-2.03597388605946	0.0609185674267399	0.139771726308962	-4.63934157315238	88	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Rian'>Rian</a>
+Mir410	-0.901221750135118	3.70006848443484	-2.03462058748079	0.0610702490918199	0.139771726308962	-4.88099717429878	208	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir410'>Mir410</a>
+3110039I08Rik	-1.63610179345525	-1.18449373319304	-2.03411361106907	0.0611271616373111	0.139771726308962	-4.41449053166305	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/3110039I08Rik'>3110039I08Rik</a>
+Jpx	1.4439778868564	-0.386376496641391	2.0256963387538	0.0620792090771524	0.141664755114062	-4.40640628270017	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Jpx'>Jpx</a>
+Ranbp3	1.65127100064997	0.13253716876798	2.01854426538914	0.0628988113300898	0.143248590274716	-4.43559297253071	21	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Ranbp3'>Ranbp3</a>
+Ano4	-1.60469225892927	-0.386376496641391	-2.01415852435434	0.0634062900341383	0.144116687109466	-4.41831749461231	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Ano4'>Ano4</a>
+Raver1-fdx1l	1.84484701704264	0.152704788521028	2.00550228504778	0.0644189220532073	0.146127216824472	-4.45962561575273	32	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Raver1-fdx1l'>Raver1-fdx1l</a>
+Mir1191	1.82343613876431	0.355147507605031	2.00159544245338	0.064880780262737	0.14678508924003	-4.47205950977787	34	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1191'>Mir1191</a>
+Snord42a	-1.13379631100394	4.75607203025783	-2.00076940150347	0.0649788196577846	0.14678508924003	-5.09261777286222	438	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord42a'>Snord42a</a>
+Elmo1	-1.44814767972568	-0.848931461409027	-1.99979301527205	0.0650948774368582	0.14678508924003	-4.45311869203765	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Elmo1'>Elmo1</a>
+B430010I23Rik	1.34949047728334	-0.986373420602892	1.99444973304055	0.0657333644405924	0.147932482892931	-4.45809589212282	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/B430010I23Rik'>B430010I23Rik</a>
+Zfp809	1.61960355427207	-0.452690836228738	1.9814089454698	0.0673157207393185	0.151195349140871	-4.47945908882588	14	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Zfp809'>Zfp809</a>
+2310050B05Rik	-1.59274071576353	-0.590132795422603	-1.97545789269397	0.0680492897692784	0.152490055886233	-4.48612649748884	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2310050B05Rik'>2310050B05Rik</a>
+Gm19705	-1.53197912631465	-1.24517208658932	-1.97349298532553	0.0682930925134662	0.152490055886233	-4.5170833713595	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm19705'>Gm19705</a>
+Mir701	-1.53197912631465	-1.24517208658932	-1.97349298532553	0.0682930925134662	0.152490055886233	-4.5170833713595	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir701'>Mir701</a>
+F630028O10Rik	-0.622888913014848	5.94290954470824	-1.96287969360653	0.0696237734116029	0.154761005415237	-5.29318401111469	928	<a href='http://www.genecards.org/index.php?path=/Search/keyword/F630028O10Rik'>F630028O10Rik</a>
+Mir223	-0.622888913014848	5.94290954470824	-1.96287969360653	0.0696237734116029	0.154761005415237	-5.29318401111469	928	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir223'>Mir223</a>
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+Mir3087	-1.55280633805545	-0.590132795422603	-1.94082835991025	0.0724641808981051	0.160546855154831	-4.54065638515475	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3087'>Mir3087</a>
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+AF357359	-1.68799855890395	1.29585702757533	-1.92491777610303	0.0745784347261457	0.163934632876851	-4.62972173041495	55	<a href='http://www.genecards.org/index.php?path=/Search/keyword/AF357359'>AF357359</a>
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+5430405H02Rik	1.78645846006788	-0.165684653346019	1.92319520065518	0.0748106549472968	0.163934632876851	-4.58774074751784	20	<a href='http://www.genecards.org/index.php?path=/Search/keyword/5430405H02Rik'>5430405H02Rik</a>
+Snora20	1.38262094231094	0.0963488416186067	1.92286428347317	0.0748553406913579	0.163934632876851	-4.56861037921303	18	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora20'>Snora20</a>
+4930519F09Rik	-1.5565120089996	-1.23129317254072	-1.9216903287951	0.0750140617025739	0.163967518012714	-4.59735520927714	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930519F09Rik'>4930519F09Rik</a>
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+A930005H10Rik	1.49847756821754	-0.371019403168199	1.89424576390839	0.0788123530754021	0.171285514017207	-4.61401782584198	14	<a href='http://www.genecards.org/index.php?path=/Search/keyword/A930005H10Rik'>A930005H10Rik</a>
+C920021L13Rik	1.45659708523928	0.785774819657178	1.89280562125827	0.0790163750358231	0.171402440904704	-4.64971051817534	32	<a href='http://www.genecards.org/index.php?path=/Search/keyword/C920021L13Rik'>C920021L13Rik</a>
+4931403E22Rik	1.70378545689415	-0.814059467696176	1.88880372983809	0.079585814935806	0.172310085088719	-4.62498282958674	16	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4931403E22Rik'>4931403E22Rik</a>
+Mir1964	-0.871113074799274	2.86663339631991	-1.88648279477582	0.0799177575555235	0.172701063202372	-4.9744960348716	105	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1964'>Mir1964</a>
+2410004N09Rik	2.12780696213311	-0.132941404588628	1.87600039224749	0.0814325355366182	0.175611886412351	-4.66535335652261	50	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2410004N09Rik'>2410004N09Rik</a>
+4930545L23Rik	1.35692949813202	-0.986373420602892	1.87504023129734	0.0815725677463155	0.175611886412351	-4.6448850582387	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930545L23Rik'>4930545L23Rik</a>
+C330022C24Rik	1.66684006383984	-0.832108206363072	1.87245175628895	0.0819511559395892	0.176094668412564	-4.64990032998496	15	<a href='http://www.genecards.org/index.php?path=/Search/keyword/C330022C24Rik'>C330022C24Rik</a>
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+Zfp410	1.71265563446791	-0.233577443974335	1.86771686993171	0.0826477630092813	0.176925136198105	-4.66576692182148	20	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Zfp410'>Zfp410</a>
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+Mir466n	1.94888590100719	1.13742198871721	1.85224203398279	0.084961673426306	0.181198634354047	-4.7515811957887	64	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir466n'>Mir466n</a>
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+Jmjd4	1.44086756566094	-0.101771470971538	1.84911253075739	0.0854366173626727	0.181532924414915	-4.69022441726304	15	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Jmjd4'>Jmjd4</a>
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+Cox18	1.25969390520503	-1.03317285995058	1.82371980602793	0.0893789810710051	0.186983832297381	-4.72463210359103	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Cox18'>Cox18</a>
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+9530080O11Rik	1.2333343214217	-1.04705177399917	1.82206906601016	0.0896408030382712	0.186983832297381	-4.72761567183742	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/9530080O11Rik'>9530080O11Rik</a>
+Gm10658	1.2333343214217	-1.04705177399917	1.82206906601016	0.0896408030382712	0.186983832297381	-4.72761567183742	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm10658'>Gm10658</a>
+AV039307	1.68466781700848	-0.822165860739921	1.8179655824626	0.0902946176139629	0.188003939229072	-4.7329903325485	18	<a href='http://www.genecards.org/index.php?path=/Search/keyword/AV039307'>AV039307</a>
+Mir653	1.31080939375484	-0.0354571313841903	1.81352557566678	0.0910068355861608	0.18914171111805	-4.73339615516883	15	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir653'>Mir653</a>
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+A330032B11Rik	1.15351830091647	-0.544811535499514	1.805581783419	0.092293585640648	0.191024884842792	-4.74543310731249	9	<a href='http://www.genecards.org/index.php?path=/Search/keyword/A330032B11Rik'>A330032B11Rik</a>
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+Mir1981	0.697255970236885	4.21228670526814	1.80136677676051	0.0929828927493876	0.191159424553245	-5.33355766780014	295	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1981'>Mir1981</a>
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+1700018L02Rik	1.60638305633868	-0.05968504002665	1.79496471819782	0.0940386190778224	0.192635663137873	-4.77706326738907	20	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1700018L02Rik'>1700018L02Rik</a>
+Rnu12	1.34545573987153	3.12465170168855	1.79074555187797	0.0947401853209974	0.193675928813183	-5.15435248901701	212	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Rnu12'>Rnu12</a>
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+AW011738	1.35994322320792	-0.986373420602892	1.78331122652731	0.0959876815075987	0.195574901071732	-4.78377188602086	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/AW011738'>AW011738</a>
+Mir1247	0.717962491463309	4.29587920045115	1.77899645447695	0.09671837092938	0.196712408610379	-5.37990996340849	300	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1247'>Mir1247</a>
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+C130046K22Rik	-1.66206124112149	-0.401145415606174	-1.77343531333303	0.0976673947466025	0.197936940330148	-4.79605188690242	13	<a href='http://www.genecards.org/index.php?path=/Search/keyword/C130046K22Rik'>C130046K22Rik</a>
+4930546K05Rik	1.23872623697392	-1.04705177399917	1.76682617714789	0.0988059745301037	0.199889391735547	-4.81031354370822	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930546K05Rik'>4930546K05Rik</a>
+Mir199a-1	1.28133340693594	0.249147894285663	1.75988001617421	0.100015250730246	0.201977701032231	-4.81578597695043	18	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199a-1'>Mir199a-1</a>
+Mir434	-0.892989649406754	5.12926720938992	-1.7580843415124	0.100329984081606	0.202255321266984	-5.5313213323858	623	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir434'>Mir434</a>
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+Mir466g	1.83795214574926	0.185777895695677	1.74292337320769	0.103022330922592	0.206606620810476	-4.86892478985408	38	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir466g'>Mir466g</a>
+D930015M05Rik	1.30968823250333	0.15849335658765	1.7428712395644	0.103031697845014	0.206606620810476	-4.83950381088453	20	<a href='http://www.genecards.org/index.php?path=/Search/keyword/D930015M05Rik'>D930015M05Rik</a>
+Mir532	0.395164755537383	7.64371024412024	1.7408125217348	0.103402190719686	0.206985788791511	-5.7782897714965	3010	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir532'>Mir532</a>
+Mir103-2	0.773766228848679	2.45632927480254	1.73913662142218	0.103704656419595	0.207227693475933	-5.11879080206363	81	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir103-2'>Mir103-2</a>
+1810014B01Rik	1.26181707046536	-1.03317285995058	1.73762861899304	0.103977485505656	0.207409634548871	-4.85288674502469	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1810014B01Rik'>1810014B01Rik</a>
+Snora69	1.22315416187213	0.909823171643444	1.73588809106924	0.104293168525467	0.207676274498356	-4.89225702628115	33	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora69'>Snora69</a>
+Zc3h14	1.41408821776149	0.00675479495901958	1.72847661834252	0.105646860853607	0.21000534535534	-4.86420908405344	19	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Zc3h14'>Zc3h14</a>
+Nkx6-2	-1.27800503999609	-0.941052160679803	-1.7146791107628	0.108208119548433	0.214722546790891	-4.8960301602504	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Nkx6-2'>Nkx6-2</a>
+Mir26b	0.351712467695003	11.5635032907349	1.7045779906641	0.110117579874109	0.21763806583767	-6.09597193580631	46666	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir26b'>Mir26b</a>
+Mir299	-0.955766682393671	1.55229988219809	-1.70455586992184	0.110121793629752	0.21763806583767	-5.00394219885035	43	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir299'>Mir299</a>
+Mir3068	-0.644710617273588	4.67886513002661	-1.70302081836154	0.110414548820487	0.21763806583767	-5.55943820497418	431	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3068'>Mir3068</a>
+4930512B01Rik	1.20898643105347	-0.682253494693378	1.70288569810342	0.110440350674856	0.21763806583767	-4.89782103905022	9	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930512B01Rik'>4930512B01Rik</a>
+Fam187b	1.23742378935899	-1.04705177399917	1.69414248393857	0.112121161065231	0.220569387543842	-4.9166784968792	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Fam187b'>Fam187b</a>
+Scarna13	1.31946224597966	-0.590132795422603	1.68885863838395	0.113147737124684	0.221824000101829	-4.91936341824324	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Scarna13'>Scarna13</a>
+Snhg10	1.31946224597966	-0.590132795422603	1.68885863838395	0.113147737124684	0.221824000101829	-4.91936341824324	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snhg10'>Snhg10</a>
+Gm10791	1.38935319993587	-0.966858520363231	1.68575319044044	0.113754902225617	0.222389287455916	-4.92671603809347	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm10791'>Gm10791</a>
+H2-K2	1.16076121091899	-1.07849411987367	1.68539104137817	0.113825892966043	0.222389287455916	-4.93053846380363	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/H2-K2'>H2-K2</a>
+Mir676	-0.437089730569779	6.48681209189413	-1.6806647861103	0.114755912374217	0.223823070117918	-5.77991725097014	1363	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir676'>Mir676</a>
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+5730422E09Rik	1.18020228563473	-0.696132408741971	1.67428783670958	0.116021244081938	0.224957555323422	-4.93882350178396	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/5730422E09Rik'>5730422E09Rik</a>
+Ythdf3	1.18280803863615	1.44825173729247	1.6741256859047	0.116053576278149	0.224957555323422	-5.03651124662328	52	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Ythdf3'>Ythdf3</a>
+C730027H18Rik	1.17258184372084	-1.07849411987367	1.67277419424211	0.116323363401244	0.224957555323422	-4.94864972108029	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/C730027H18Rik'>C730027H18Rik</a>
+Gm8615	1.17258184372084	-1.07849411987367	1.67277419424211	0.116323363401244	0.224957555323422	-4.94864972108029	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm8615'>Gm8615</a>
+2900009J06Rik	1.34828416289482	-0.986373420602892	1.66877503516158	0.117124882491955	0.226124350124061	-4.9510598544989	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2900009J06Rik'>2900009J06Rik</a>
+Rnf44	2.04490507739992	1.01150037846895	1.66529647991714	0.117825963606828	0.227093622424646	-5.02208296723603	88	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Rnf44'>Rnf44</a>
+A630010A05Rik	-1.25675269332335	0.631280460684989	-1.66260430434796	0.118371056366922	0.227453417799216	-4.9530858854327	24	<a href='http://www.genecards.org/index.php?path=/Search/keyword/A630010A05Rik'>A630010A05Rik</a>
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+4933417D19Rik	1.18269745295452	-1.07849411987367	1.65430499284386	0.120065250928896	0.229856461929313	-4.97500052644218	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4933417D19Rik'>4933417D19Rik</a>
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+1110020A21Rik	1.25194593270892	-0.49237610996076	1.63876864711163	0.123293382787791	0.235247073178712	-4.9892549623361	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1110020A21Rik'>1110020A21Rik</a>
+Alg11	1.32531249978621	-0.590132795422603	1.6361767652414	0.123839170710122	0.235510431606847	-4.99444823996257	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Alg11'>Alg11</a>
+Vaultrc5	-0.448072317249509	7.10631262637587	-1.63615281653852	0.123844223456712	0.235510431606847	-5.89478683307987	2022	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Vaultrc5'>Vaultrc5</a>
+Mir3060	-1.21202833172584	0.27171942499089	-1.6351645637142	0.124052882574934	0.235514707184691	-4.96812309442586	19	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3060'>Mir3060</a>
+Mir1955	1.13186286307835	-0.682253494693378	1.63345540817796	0.124414470052149	0.235669705476309	-4.9969826223679	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1955'>Mir1955</a>
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+C730036E19Rik	1.2943846006491	-1.01217978028632	1.63063554865266	0.125013028232036	0.236158717239657	-5.00596783361666	9	<a href='http://www.genecards.org/index.php?path=/Search/keyword/C730036E19Rik'>C730036E19Rik</a>
+4930405P13Rik	1.34966504178449	-0.986373420602892	1.62725241064407	0.125734431753086	0.236979623633452	-5.00991537352707	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930405P13Rik'>4930405P13Rik</a>
+Dancr	1.3062030182448	1.18459288047694	1.62665135682264	0.125862972762377	0.236979623633452	-5.07677615617175	48	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Dancr'>Dancr</a>
+Ankrd11	1.37844840409545	1.82869495288249	1.62469304300553	0.126282563660683	0.237377932680131	-5.15746897731049	86	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Ankrd11'>Ankrd11</a>
+2610020C07Rik	1.50920105232855	-0.317940522228579	1.6135231103667	0.128698986652833	0.241522275938952	-5.03116671787619	19	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2610020C07Rik'>2610020C07Rik</a>
+1600002D24Rik	-1.25321204977434	-0.756810762138252	-1.61125552509827	0.12919437339977	0.242053826024856	-5.03110633443407	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1600002D24Rik'>1600002D24Rik</a>
+BC031361	1.03166169729911	-1.13917247326995	1.608779945121	0.129737072495046	0.242672130683356	-5.043580985531	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/BC031361'>BC031361</a>
+5730408K05Rik	1.05171391832391	-1.13917247326995	1.60382914837461	0.130828274941307	0.244312703286467	-5.05048396234822	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/5730408K05Rik'>5730408K05Rik</a>
+4833422C13Rik	1.56072686239259	0.473647969476496	1.59330634063312	0.133173818859074	0.248286482546083	-5.0792948158275	34	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4833422C13Rik'>4833422C13Rik</a>
+Mir15b	-0.423479234767332	6.16430836474156	-1.59205186812547	0.133455834392276	0.248406373640436	-5.88344797905857	1064	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir15b'>Mir15b</a>
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+2700089E24Rik	1.9346637528719	0.708144926037837	1.59009813142159	0.13389606984202	0.248415310064625	-5.10719912908875	70	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2700089E24Rik'>2700089E24Rik</a>
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+4930474G06Rik	-1.090892671974	-1.03317285995058	-1.58193904835456	0.135748030192849	0.250441466610603	-5.09374604062072	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930474G06Rik'>4930474G06Rik</a>
+A430093F15Rik	-1.090892671974	-1.03317285995058	-1.58193904835456	0.135748030192849	0.250441466610603	-5.09374604062072	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/A430093F15Rik'>A430093F15Rik</a>
+Rreb1	1.35338804346774	2.10846654001091	1.58142192959551	0.135866141833447	0.250441466610603	-5.26419259030567	113	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Rreb1'>Rreb1</a>
+Mir485	-1.2897278302183	-0.360570136957963	-1.57792310950414	0.136667596032013	0.250873719680857	-5.05792690495308	13	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir485'>Mir485</a>
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+9230112J17Rik	-1.01261850877746	-1.42941348513087	-1.56975595848976	0.138554138577694	0.251258367802273	-5.13526440107113	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/9230112J17Rik'>9230112J17Rik</a>
+Mir3100	-1.01261850877746	-1.42941348513087	-1.56975595848976	0.138554138577694	0.251258367802273	-5.13526440107113	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3100'>Mir3100</a>
+Mir294	1.03626141233244	-1.13917247326995	1.56969188750367	0.138569025899642	0.251258367802273	-5.09768561064634	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir294'>Mir294</a>
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+Mir129-1	1.05464886354904	-1.13917247326995	1.56899253420323	0.138731614123954	0.251258367802273	-5.09864530153619	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir129-1'>Mir129-1</a>
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+4930451G09Rik	1.06510899754063	-1.13917247326995	1.56184533087519	0.140402574895956	0.252848126899102	-5.10843610513404	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930451G09Rik'>4930451G09Rik</a>
+4933421O10Rik	1.06510899754063	-1.13917247326995	1.56184533087519	0.140402574895956	0.252848126899102	-5.10843610513404	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4933421O10Rik'>4933421O10Rik</a>
+St5	1.16930236967868	0.570831252021079	1.5614487016406	0.140495804078905	0.252848126899102	-5.1040121162741	24	<a href='http://www.genecards.org/index.php?path=/Search/keyword/St5'>St5</a>
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+Mir3069	1.1967490330554	-0.650811148818883	1.55602233545589	0.141776597800618	0.25395148836814	-5.10475733476948	9	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3069'>Mir3069</a>
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+4932702P03Rik	1.50538536018542	-0.190947829244951	1.54735549642484	0.143842852742846	0.256846158027523	-5.12545513466049	20	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4932702P03Rik'>4932702P03Rik</a>
+Mir341	-1.11910417431075	-0.268449437687187	-1.54504024071338	0.144399143660684	0.257436598307563	-5.09444510471904	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir341'>Mir341</a>
+Fam19a2	-1.08108870526458	-1.03317285995058	-1.54274205574173	0.144953138847169	0.258021109866802	-5.14743110946704	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Fam19a2'>Fam19a2</a>
+Mir2137	-1.25397648150412	-0.986373420602892	-1.53902949676667	0.145851890715621	0.259216522284305	-5.1478345461744	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir2137'>Mir2137</a>
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+Elp3	-1.44496494213962	1.49755589579473	-1.53456064882656	0.146939992809584	0.260339335086546	-5.2298474338907	55	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Elp3'>Elp3</a>
+Six3os1	-1.3837215389721	-1.31472125515486	-1.53340154891498	0.147223338498394	0.260436944537469	-5.17353312572401	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Six3os1'>Six3os1</a>
+Rmst	-1.34494122456533	-0.508623208350141	-1.52875491880875	0.148363873123417	0.262048265067831	-5.13210633012727	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Rmst'>Rmst</a>
+4930564K09Rik	1.15715309457904	-1.07849411987367	1.51860435848876	0.150881394880579	0.266082954495736	-5.16248906856691	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930564K09Rik'>4930564K09Rik</a>
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+Mir200c	1.09203191538954	1.0686845390219	1.51301819802264	0.152282191329828	0.267725701552132	-5.21562223006706	43	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200c'>Mir200c</a>
+Mir500	-0.959184822315059	1.55556768404836	-1.50996567016574	0.153052273761653	0.268308865049533	-5.27805724838699	47	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir500'>Mir500</a>
+Brd2	1.15193277255657	1.46278337085446	1.5098394012633	0.153084199077341	0.268308865049533	-5.26772609337448	52	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Brd2'>Brd2</a>
+1700061I17Rik	-0.993032112528657	-1.07849411987367	-1.5078450002038	0.153589200235581	0.268618908035033	-5.19885089576796	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1700061I17Rik'>1700061I17Rik</a>
+2010009K17Rik	1.39848757206625	0.0129207590044654	1.50658142705804	0.153909874663779	0.268618908035033	-5.1753515727655	21	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2010009K17Rik'>2010009K17Rik</a>
+4930549G23Rik	1.15784945023494	-1.07849411987367	1.50450440196419	0.154438215311991	0.268618908035033	-5.18132752967772	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930549G23Rik'>4930549G23Rik</a>
+Arfrp1	1.15784945023494	-1.07849411987367	1.50450440196419	0.154438215311991	0.268618908035033	-5.18132752967772	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Arfrp1'>Arfrp1</a>
+Gm16675	1.15784945023494	-1.07849411987367	1.50450440196419	0.154438215311991	0.268618908035033	-5.18132752967772	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm16675'>Gm16675</a>
+9230116N13Rik	1.06454128715679	-1.13917247326995	1.50290619358259	0.154845796366435	0.268917889884478	-5.18797830371707	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/9230116N13Rik'>9230116N13Rik</a>
+4930515G01Rik	0.992431794232819	-0.788253108012747	1.49297552868103	0.157398682710309	0.272936013635962	-5.18861224143696	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930515G01Rik'>4930515G01Rik</a>
+Mir381	-0.585788303821621	4.02795786800028	-1.48635287193065	0.159120749771416	0.275503452942618	-5.77368217940814	263	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir381'>Mir381</a>
+Mir377	-1.26023741335144	-0.742931848089659	-1.46946309676428	0.163584151533594	0.282783957164269	-5.22241603606054	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir377'>Mir377</a>
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[phone]Rik	1.1439446656217	-0.676617508502311	1.43366062517497	0.173391617780733	0.295283337145994	-5.26641582277432	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/9330162012Rik'>9330162012Rik</a>
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+4930455H04Rik	1.13172981083616	-0.682253494693378	1.40835127249367	0.180614676369773	0.303507136580134	-5.29864005434158	9	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930455H04Rik'>4930455H04Rik</a>
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+Mir363	1.15445492135561	-0.478497195912167	1.29452460128447	0.216207564177154	0.349918908831395	-5.43848438880553	13	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir363'>Mir363</a>
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+9330178D15Rik	-1.05713219200343	-1.07849411987367	-1.27002691260158	0.224559037706864	0.360875862004974	-5.49789518736927	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/9330178D15Rik'>9330178D15Rik</a>
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+Mir1970	0.981623687672708	-1.16497883295338	1.23358760674581	0.237451560697612	0.377869220022281	-5.52422742180909	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1970'>Mir1970</a>
+4933433G15Rik	-0.845091810799975	-1.13917247326995	-1.21970156103377	0.242514607267494	0.384823868748979	-5.56216873762972	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4933433G15Rik'>4933433G15Rik</a>
+Mir487b	-0.845091810799975	-1.13917247326995	-1.21970156103377	0.242514607267494	0.384823868748979	-5.56216873762972	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir487b'>Mir487b</a>
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+Mir744	0.375928995244175	7.06487761533261	1.21046077244345	0.245930308976254	0.388148264070044	-6.45312420350352	2175	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir744'>Mir744</a>
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+Gm10336	-0.862983197557129	-1.13917247326995	-1.19601713252826	0.251343875564565	0.393012592445325	-5.58891156888004	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm10336'>Gm10336</a>
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+Dennd2d	0.921530541409756	-1.19510484539135	1.19301988845778	0.25247872941492	0.393012592445325	-5.57311877933865	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Dennd2d'>Dennd2d</a>
+Gm14403	0.921530541409756	-1.19510484539135	1.19301988845778	0.25247872941492	0.393012592445325	-5.57311877933865	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm14403'>Gm14403</a>
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+Mir211	0.825074748111626	-0.880373807283523	1.17378618405685	0.259855584968479	0.40284676963184	-5.57990075138058	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir211'>Mir211</a>
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+1500015L24Rik	0.808616217238156	-1.24517208658932	1.16726413306531	0.262394269069057	0.404583595956478	-5.60687790222948	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1500015L24Rik'>1500015L24Rik</a>
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+Trpt1	0.808616217238156	-1.24517208658932	1.16726413306531	0.262394269069057	0.404583595956478	-5.60687790222948	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Trpt1'>Trpt1</a>
+BC029722	0.823443920149512	-1.23129317254072	1.16607728334613	0.262858281841981	0.404752091203375	-5.60671637501778	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/BC029722'>BC029722</a>
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+Mir3058	-0.978203405704609	-0.498012096151827	-1.14953116886071	0.269392696348615	0.411904246746464	-5.58396014066336	9	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3058'>Mir3058</a>
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+Mir376b	-0.99103045209925	1.03829066633399	-1.14279150067575	0.272089498256322	0.414737087115015	-5.63858333409662	42	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir376b'>Mir376b</a>
+Mir30a	-0.151237258601805	15.2301476884988	-1.14239018110005	0.272250725897586	0.414737087115015	-7.0852176231084	565907	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir30a'>Mir30a</a>
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+2610001J05Rik	-0.86697193885018	-0.544811535499514	-1.14000047811695	0.273212275243521	0.415093483425908	-5.59553124660726	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2610001J05Rik'>2610001J05Rik</a>
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+Mir1965	-0.872346376244262	-0.941052160679803	-1.1314437021438	0.276676392456387	0.417576407133251	-5.64344814416069	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1965'>Mir1965</a>
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+Gm10649	-0.892846942526544	-0.742931848089659	-1.09635581501043	0.291228443757408	0.437316695864095	-5.65951959369185	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm10649'>Gm10649</a>
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+Mirg	-0.474362072277141	6.82767679984071	-1.08788511862449	0.294825638847012	0.44112747945308	-6.57223781945416	1940	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mirg'>Mirg</a>
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+9430060I03Rik	0.893039869828009	-0.484133182103234	1.08424508768217	0.296381529077199	0.441769310816773	-5.66824954289941	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/9430060I03Rik'>9430060I03Rik</a>
+Mphosph9	0.825946492812557	-0.835052547360434	1.08364147818961	0.296640122891534	0.441769310816773	-5.67407248575821	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mphosph9'>Mphosph9</a>
+Mir465	0.753847528822331	-1.27661443246381	1.08288371043005	0.296964996841775	0.441769310816773	-5.70008050633046	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir465'>Mir465</a>
+Mir7-1	-0.462285314925654	2.79727444411883	-1.07768367150356	0.299201499765338	0.444023980943917	-6.04570260584071	96	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir7-1'>Mir7-1</a>
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+4930414N06Rik	0.732304356782422	-1.27661443246381	1.07567328957759	0.300069484201389	0.444071701003612	-5.70749397255429	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930414N06Rik'>4930414N06Rik</a>
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+Mir880	0.798518477299392	-1.27661443246381	1.06858448026948	0.303144932062895	0.446380139558595	-5.7147416680859	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir880'>Mir880</a>
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+F630206G17Rik	0.759617567138328	-1.27661443246381	1.06479234302223	0.304799642362463	0.447013357243663	-5.7186021728347	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/F630206G17Rik'>F630206G17Rik</a>
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+4930565N06Rik	-0.760881657711942	-0.452690836228738	-1.04536813721085	0.313379640481894	0.455414522982691	-5.68467326756101	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930565N06Rik'>4930565N06Rik</a>
+Gm19782	-0.824138055093141	-1.04705177399917	-1.04419216716558	0.313904694022045	0.455414522982691	-5.74437221530442	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm19782'>Gm19782</a>
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+Mir672	-0.747248291924879	-1.04705177399917	-1.04198352749126	0.314892552981749	0.455414522982691	-5.74657924729597	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir672'>Mir672</a>
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+2610307P16Rik	-0.91429583632135	-0.954931074728396	-1.03725537976782	0.317014922908806	0.457287012691463	-5.74201320442599	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2610307P16Rik'>2610307P16Rik</a>
+B630019K06Rik	0.719990612273558	-0.756810762138252	1.03218755693734	0.319301294119003	0.46000350579518	-5.72479023365126	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/B630019K06Rik'>B630019K06Rik</a>
+Gm14872	0.835812662260224	-0.835052547360434	1.03077941192774	0.319938704270154	0.460340556837637	-5.72736949007166	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm14872'>Gm14872</a>
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+Gm19461	0.915494510219759	-0.788253108012747	1.02058918961822	0.324578899608511	0.465842169123662	-5.73572336698256	11	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm19461'>Gm19461</a>
+Mir702	-0.826707259520221	-0.299891783561682	-1.01839078954777	0.325586298913891	0.465882836241176	-5.70404861077289	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir702'>Mir702</a>
+E130307A14Rik	-0.788814584438982	-0.590132795422603	-1.01803072764692	0.325751509050542	0.465882836241176	-5.72282760292051	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/E130307A14Rik'>E130307A14Rik</a>
+Mir677	-0.46535805282509	2.7048223776038	-1.01785498662811	0.325832167677878	0.465882836241176	-6.08983176917819	94	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir677'>Mir677</a>
+2900008C10Rik	-0.828374176793865	-0.558690449548107	-1.01087466362321	0.329047523081663	0.469891394037769	-5.72790706263801	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2900008C10Rik'>2900008C10Rik</a>
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+Snord7	-0.835470371413723	-0.676617508502311	-1.00141282716469	0.333442241670381	0.474978274339456	-5.74740702860384	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord7'>Snord7</a>
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+Kcnq1ot1	0.910278085334024	-0.218382196489221	0.997758138243239	0.335150923261523	0.476223167423908	-5.74375068180754	16	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Kcnq1ot1'>Kcnq1ot1</a>
+4921513I03Rik	-0.898652409766853	-0.954931074728396	-0.996357559472656	0.335807392489445	0.476352069705573	-5.7819683962692	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4921513I03Rik'>4921513I03Rik</a>
+Snord111	0.487167361404432	2.40322325564047	0.995476712980872	0.336220726321058	0.476352069705573	-6.04721452535901	82	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord111'>Snord111</a>
+Mir326	-0.382358415670825	3.27011368251419	-0.994342337417545	0.336753562180123	0.476352069705573	-6.21830968460093	144	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir326'>Mir326</a>
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+4930573O16Rik	0.724242940462577	-0.880373807283523	0.988574355151803	0.33947219472701	0.478785876617451	-5.77014512800664	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930573O16Rik'>4930573O16Rik</a>
+C030016D13Rik	0.736627595056793	-0.880373807283523	0.98365906844454	0.341801211615667	0.48147553389318	-5.7748146431183	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/C030016D13Rik'>C030016D13Rik</a>
+Mir106b	-0.272040824179646	6.30534021503053	-0.978912859532382	0.344060849311784	0.483787015120022	-6.6415010931846	1230	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir106b'>Mir106b</a>
+Mir93	0.231991919214371	8.92958242253252	0.978432473677121	0.344290145729586	0.483787015120022	-6.83817344932306	7480	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir93'>Mir93</a>
+A130049A11Rik	0.749480333675935	-0.90486383353043	0.973825967230468	0.346494399579791	0.485688095725481	-5.78593949448688	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/A130049A11Rik'>A130049A11Rik</a>
+Ppp4r1l-ps	0.749480333675935	-0.90486383353043	0.973825967230468	0.346494399579791	0.485688095725481	-5.78593949448688	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Ppp4r1l-ps'>Ppp4r1l-ps</a>
+Snora44	0.286033309288083	5.62130667581717	0.971157099851877	0.3477760255746	0.48688643580444	-6.58548506620032	724	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora44'>Snora44</a>
+Kat5	0.866499552085197	-0.402623595030772	0.964975242015777	0.35075746085532	0.490458655436177	-5.78144072211864	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Kat5'>Kat5</a>
+Osbpl1a	1.09737003164025	0.516465901027703	0.963410623524111	0.351514898897857	0.490916156233114	-5.78884397041858	52	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Osbpl1a'>Osbpl1a</a>
+Mir1982	0.739352688973082	0.294469154208751	0.962125981745475	0.35213765737009	0.491184678556568	-5.76656609837178	17	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1982'>Mir1982</a>
+Asb7	0.703526575105393	-0.925695067206612	0.958123449514082	0.354082936025685	0.492563942310599	-5.80224617247519	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Asb7'>Asb7</a>
+Hdac10	0.974865932277475	-1.17447243960754	0.957964659851365	0.354160264679881	0.492563942310599	-5.81150986834852	18	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Hdac10'>Hdac10</a>
+Brat1	0.726590679354257	-0.880373807283523	0.957428291454004	0.354421557087644	0.492563942310599	-5.79939146334398	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Brat1'>Brat1</a>
+Mir491	-0.684898615634921	-0.835052547360435	-0.953861551192324	0.35616253103266	0.494381323489374	-5.80900377777519	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir491'>Mir491</a>
+Pum2	0.976211707535353	0.893848485511468	0.941843079399731	0.362072854082899	0.501974637312986	-5.83976051882873	52	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Pum2'>Pum2</a>
+Flcn	0.819178463384112	0.21104107159461	0.936286718836365	0.364828219319466	0.505180823111056	-5.78834781376735	22	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Flcn'>Flcn</a>
+2310010J17Rik	-0.781496807473563	-0.752064780863374	-0.934867786030351	0.365534182055843	0.505544850576626	-5.81765744708763	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2310010J17Rik'>2310010J17Rik</a>
+Yipf2	0.803138506076097	-0.880373807283523	0.933170155190723	0.366380047226091	0.506101251676719	-5.82160275803741	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Yipf2'>Yipf2</a>
+Pex11b	0.745690782417397	-0.742931848089659	0.932131479018354	0.366898247195751	0.506204232225335	-5.81894124952379	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Pex11b'>Pex11b</a>
+Mir301b	-0.741931823310326	0.0963488416186067	-0.928572452406972	0.368677700638315	0.507450144605635	-5.78347200652652	14	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir301b'>Mir301b</a>
+Mir3066	-0.837579077861343	-0.558690449548107	-0.927767726846745	0.369080873917973	0.507450144605635	-5.80554388805339	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3066'>Mir3066</a>
+1110054M08Rik	0.762586926696282	-0.108062930415306	0.927658715560211	0.369135512728026	0.507450144605635	-5.79933690871854	16	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1110054M08Rik'>1110054M08Rik</a>
+2810008D09Rik	0.62387744108405	2.75194116634391	0.919384284757436	0.373299112497706	0.512041876787549	-6.18722980685037	137	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2810008D09Rik'>2810008D09Rik</a>
+Gm5512	0.771365549912191	-0.452690836228738	0.919237589387622	0.373373217780228	0.512041876787549	-5.82241315825623	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5512'>Gm5512</a>
+Rbbp8	0.886305125756175	-0.0477575943918147	0.917555243290929	0.374223801048332	0.512592265301497	-5.81282466752688	18	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Rbbp8'>Rbbp8</a>
+Gm11974	0.778082873591224	-0.447944854953861	0.909892000761802	0.37811508552564	0.517301334034479	-5.83079148689953	11	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm11974'>Gm11974</a>
+Mir369	-0.74269677210509	0.589456147344549	-0.905344093956725	0.380437470711399	0.519596997836352	-5.82156063054654	26	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir369'>Mir369</a>
+Mir26a-2	0.485967334173185	2.96081541822386	0.904823661302764	0.380703847669755	0.519596997836352	-6.23863459210439	131	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir26a-2'>Mir26a-2</a>
+Minos1	0.704827095217255	0.326231814341724	0.900400917247283	0.382972698552506	0.522069114753178	-5.81919593446542	22	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Minos1'>Minos1</a>
+Deaf1	0.779036313891313	-0.299891783561682	0.896459320434846	0.385002448889921	0.524209778261814	-5.83491078724319	14	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Deaf1'>Deaf1</a>
+Gm19466	-0.749840672361975	-1.04705177399917	-0.887587437647754	0.389597708777317	0.529834309552942	-5.89076869788414	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm19466'>Gm19466</a>
+Gm2518	0.63646451042641	-0.558690449548107	0.883457449799982	0.391749438497377	0.532126320625604	-5.85297878336349	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm2518'>Gm2518</a>
+Mir505	0.574628179268003	0.386589853479527	0.877080062325064	0.395087742631044	0.535616337424576	-5.8408806452811	16	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir505'>Mir505</a>
+Gm13483	-0.650881842270608	-1.13917247326995	-0.876756483145742	0.395257630246707	0.535616337424576	-5.90961874985058	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm13483'>Gm13483</a>
+A930016O22Rik	-0.909159760956733	-0.165684653346019	-0.874712631220314	0.39633183750076	0.535965610314034	-5.83382312143566	20	<a href='http://www.genecards.org/index.php?path=/Search/keyword/A930016O22Rik'>A930016O22Rik</a>
+4930526L06Rik	-0.646483610508766	-1.13917247326995	-0.874478831554822	0.39645484233571	0.535965610314034	-5.91157337325639	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930526L06Rik'>4930526L06Rik</a>
+1500011K16Rik	0.687958770706193	-0.941052160679803	0.866684426419982	0.400570191138535	0.540789721466861	-5.88463986982684	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1500011K16Rik'>1500011K16Rik</a>
+Adamts10	0.766269359657236	-0.742931848089659	0.865927841035999	0.400971169466226	0.540789721466861	-5.87691249385262	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Adamts10'>Adamts10</a>
+Mir206	-0.641735198874169	-1.04705177399917	-0.859684053228752	0.404290476936943	0.544080673710294	-5.91464885848361	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir206'>Mir206</a>
+Mirlet7a-1	0.288440707007994	4.74252865689731	0.859544351286645	0.404364952941568	0.544080673710294	-6.58293245452761	419	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mirlet7a-1'>Mirlet7a-1</a>
+Mir382	-0.527248187537959	0.0495494022709194	-0.854532688517629	0.407042720034116	0.547038567207216	-5.84404452207965	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir382'>Mir382</a>
+Snord73a	0.572583034995795	1.81609219396321	0.851752202751694	0.408533400862583	0.548396012216715	-6.06031448455445	64	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord73a'>Snord73a</a>
+AI450353	-0.739501717206301	-0.628239618113655	-0.84525729275282	0.412029489929552	0.551965918621367	-5.88226286676174	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/AI450353'>AI450353</a>
+Rnf126	0.61640700457571	-0.941052160679803	0.844020033078334	0.412697708943189	0.551965918621367	-5.90363669815116	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Rnf126'>Rnf126</a>
+4930452A19Rik	-0.567623714118899	-1.13917247326995	-0.842981854548559	0.41325895737657	0.551965918621367	-5.93813552591444	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930452A19Rik'>4930452A19Rik</a>
+Mir20b	-0.567623714118899	-1.13917247326995	-0.842981854548559	0.41325895737657	0.551965918621367	-5.93813552591444	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir20b'>Mir20b</a>
+Gm20757	-0.731130631705067	-1.04705177399917	-0.842329981431555	0.41361162175396	0.551965918621367	-5.92915547644012	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm20757'>Gm20757</a>
+4931431C16Rik	-0.591970897908513	-0.484133182103234	-0.841074383427949	0.414291458744729	0.552203761888197	-5.87182267817147	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4931431C16Rik'>4931431C16Rik</a>
+Mir541	-0.389131733074012	6.47782397759286	-0.840213916014968	0.414757777334079	0.552203761888197	-6.78224992188811	1553	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir541'>Mir541</a>
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+Snapc4	0.677537959473713	-0.941052160679803	0.838048077598245	0.41593304616484	0.552479168421516	-5.90856686178304	9	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snapc4'>Snapc4</a>
+2210408F21Rik	0.673125158878238	3.63276510319773	0.835452055835978	0.417344619062095	0.553709546918431	-6.41859057863293	234	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2210408F21Rik'>2210408F21Rik</a>
+Gm10865	0.652530700740246	-0.558690449548107	0.834529610770428	0.417846946728652	0.553732132656668	-5.8940864123663	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm10865'>Gm10865</a>
+Lmf1	-0.698964865722747	-0.133213816846033	-0.831214508127132	0.419655480523413	0.555440326826189	-5.86465518441044	13	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Lmf1'>Lmf1</a>
+B230208H11Rik	-0.324105163507426	4.07425728624104	-0.830383638654244	0.42010955482121	0.555440326826189	-6.51194043474033	250	<a href='http://www.genecards.org/index.php?path=/Search/keyword/B230208H11Rik'>B230208H11Rik</a>
+Zfp207	0.813007063755825	-0.0836318824890616	0.828134659773233	0.421340237870797	0.556422698391875	-5.88719575711569	19	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Zfp207'>Zfp207</a>
+Mir1945	0.597491165734377	-0.941052160679803	0.826047545337222	0.422484441705835	0.557288725995789	-5.91837835814761	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1945'>Mir1945</a>
+Snora41	0.348564473053555	4.54185649419262	0.819592789265972	0.426035844548422	0.560279811338197	-6.58753509611365	394	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora41'>Snora41</a>
+Oxsr1	0.724767749665156	0.244978069667359	0.819331396413772	0.426180068646681	0.560279811338197	-5.88476749078111	24	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Oxsr1'>Oxsr1</a>
+D630024D03Rik	0.728476694326676	-1.31472125515486	0.818971143090679	0.426378890981613	0.560279811338197	-5.94729714256845	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/D630024D03Rik'>D630024D03Rik</a>
+4933400L20Rik	0.515324865407562	-1.03317285995058	0.818083247017312	0.426869173233144	0.560279811338197	-5.9337772796173	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4933400L20Rik'>4933400L20Rik</a>
+Xist	0.723357937638788	-1.31472125515486	0.816666748076131	0.427652095638525	0.560279811338197	-5.94915534796961	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Xist'>Xist</a>
+Dlg1	0.603909137429248	1.27329048309733	0.815752808761627	0.428157736836546	0.560279811338197	-5.99440605481118	45	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Dlg1'>Dlg1</a>
+March2	0.877263658846623	0.62903919856468	0.815695775265458	0.428189303669507	0.560279811338197	-5.91500249911908	36	<a href='http://www.genecards.org/index.php?path=/Search/keyword/March2'>March2</a>
+C230037L18Rik	0.602090880767705	-0.941052160679803	0.813307514125875	0.429512503460807	0.561367430067332	-5.92865426872929	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/C230037L18Rik'>C230037L18Rik</a>
+Gm13375	0.630370755592059	-0.941052160679803	0.811990507037629	0.430243308062424	0.561679192790876	-5.9297082862367	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm13375'>Gm13375</a>
+Gt(ROSA)26Sor	-0.733479640637234	0.703375227668527	-0.811102967738619	0.430736253048963	0.561680073975848	-5.91552151445348	26	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gt(ROSA)26Sor'>Gt(ROSA)26Sor</a>
+Mir16-1	0.23749541505541	5.06012981661098	0.809632974888138	0.431553495333911	0.562103354082183	-6.66710805508667	499	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir16-1'>Mir16-1</a>
+4930523C07Rik	0.594215392165458	-0.544811535499514	0.807761652304698	0.432595297587676	0.562150931706581	-5.915729457308	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930523C07Rik'>4930523C07Rik</a>
+Mir374	0.289766495627774	4.44733832008286	0.806913394226144	0.433068070964141	0.562150931706581	-6.58616786299793	323	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir374'>Mir374</a>
+Mir374c	0.289766495627774	4.44733832008286	0.806913394226144	0.433068070964141	0.562150931706581	-6.58616786299793	323	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir374c'>Mir374c</a>
+Mir32	0.284410784956249	4.15923774757354	0.802255193307119	0.435670204852205	0.564332305440744	-6.54373122401893	274	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir32'>Mir32</a>
+4930481A15Rik	0.749607671194882	-0.676617508502311	0.802134533319532	0.435737739783782	0.564332305440744	-5.92746695739246	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930481A15Rik'>4930481A15Rik</a>
+Mir409	-0.359607138432163	2.88484526509054	-0.797779273016708	0.438179914112214	0.566851793653103	-6.32177877712439	114	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir409'>Mir409</a>
+Cdh23	0.599378997186575	-0.00965077170076204	0.794288413364285	0.440143672025998	0.568747372346165	-5.90268758787859	14	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Cdh23'>Cdh23</a>
+Mir187	-0.410978066923546	2.47994750376	-0.791106453483068	0.441938529712543	0.570420658825805	-6.25179118381728	82	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir187'>Mir187</a>
+1700012D01Rik	0.583673007317414	-0.544811535499514	0.784412244834506	0.445729690119356	0.574663928165181	-5.93404385599654	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1700012D01Rik'>1700012D01Rik</a>
+Tubgcp4	0.664451553261744	-0.360570136957963	0.781428132053519	0.447426298647817	0.576200233360225	-5.92858125197625	13	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Tubgcp4'>Tubgcp4</a>
+D930016D06Rik	0.626414726591185	-0.925695067206612	0.770815021447429	0.453493261191949	0.58335491659528	-5.9606398937825	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/D930016D06Rik'>D930016D06Rik</a>
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+8430429K09Rik	0.414916540751085	-0.788253108012747	0.512906371671284	0.615928717589278	0.728263903387944	-6.12271326702371	11	<a href='http://www.genecards.org/index.php?path=/Search/keyword/8430429K09Rik'>8430429K09Rik</a>
+Fbxo34	0.40198566998122	0.1102277556672	0.509352622996849	0.618354078512004	0.730374744909107	-6.08031249836236	15	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Fbxo34'>Fbxo34</a>
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+Abhd10	-0.374596139874294	-0.63693223477029	-0.499427866618794	0.625151920071888	0.736262362403135	-6.11479367410621	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Abhd10'>Abhd10</a>
+Gm6793	0.389273388584781	-1.03317285995058	0.498559841769692	0.625748160602701	0.736262362403135	-6.14405724031514	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm6793'>Gm6793</a>
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+Gm15545	-0.330712612254716	-1.03317285995058	-0.495988985275263	0.627515656816932	0.736611523333955	-6.15804139536778	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm15545'>Gm15545</a>
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+Mir423	-0.173689502560178	8.7519993946383	-0.492479800459781	0.629932094687387	0.736611523333955	-7.19207867477127	6997	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir423'>Mir423</a>
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+2610027K06Rik	0.418297137532964	-0.478497195912167	0.491895430681986	0.630334921865253	0.736611523333955	-6.11191956714245	11	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2610027K06Rik'>2610027K06Rik</a>
+Mir147	-0.328652468204269	-1.03317285995058	-0.491676373837183	0.630485957074276	0.736611523333955	-6.16020521199643	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir147'>Mir147</a>
+Gm5095	-0.324568459168512	-1.03317285995058	-0.490626195985013	0.631210270949685	0.736611523333955	-6.16072936854254	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5095'>Gm5095</a>
+Gm9776	0.388741227193178	-0.941052160679803	0.490378296979785	0.631381305714819	0.736611523333955	-6.1463267385683	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm9776'>Gm9776</a>
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+Mir30c-2	0.137775378234264	6.42581414345931	0.485294592286323	0.634893559111238	0.739197500965227	-7.01980953500918	1345	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir30c-2'>Mir30c-2</a>
+4930555B11Rik	0.2949397151298	1.99987508225673	0.483042377674677	0.636452504372091	0.740257194177937	-6.35317786250865	61	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930555B11Rik'>4930555B11Rik</a>
+Mir667	-0.391305201966948	-0.848931461409027	-0.475887236012698	0.641417003923651	0.745271691931656	-6.14780781181069	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir667'>Mir667</a>
+A930015D03Rik	0.376646313021944	0.514898879899676	0.473277554456916	0.643232148337921	0.745696184804009	-6.11541875955504	22	<a href='http://www.genecards.org/index.php?path=/Search/keyword/A930015D03Rik'>A930015D03Rik</a>
+Mir148b	-0.096502203766917	9.5098882524752	-0.472634911746632	0.643679496834764	0.745696184804009	-7.2530384831483	10703	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148b'>Mir148b</a>
+Mir5114	-0.355477405873343	-0.848931461409028	-0.472543728748277	0.643742981623093	0.745696184804009	-6.14941854830243	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir5114'>Mir5114</a>
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+Mir3473	-0.35240146171116	-0.63693223477029	-0.461057879770776	0.651762750418594	0.752701819182497	-6.13347427347714	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3473'>Mir3473</a>
+6330549D23Rik	-0.331449829799571	-0.254570523638594	-0.461047742280118	0.651769848687385	0.752701819182497	-6.10197272310564	9	<a href='http://www.genecards.org/index.php?path=/Search/keyword/6330549D23Rik'>6330549D23Rik</a>
+2810001G20Rik	-0.295155201235964	-1.24517208658932	-0.455859206316244	0.655407440132046	0.756137400597235	-6.19832965924427	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2810001G20Rik'>2810001G20Rik</a>
+Plscr3	-0.307745114670155	-1.03317285995058	-0.449268914134516	0.660040873119404	0.760713773968929	-6.18050852643307	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Plscr3'>Plscr3</a>
+Mir130a	0.0948947867813811	9.53816266066212	0.446663133142086	0.661876928287154	0.762060116221638	-7.26729031205233	11048	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir130a'>Mir130a</a>
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+A430071A18Rik	-0.354071454044044	-1.24517208658932	-0.433473215739963	0.671205080288204	0.770467803429417	-6.20849188803248	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/A430071A18Rik'>A430071A18Rik</a>
+Cd22	-0.354071454044044	-1.24517208658932	-0.433473215739963	0.671205080288204	0.770467803429417	-6.20849188803248	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Cd22'>Cd22</a>
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+4930426L09Rik	0.280363052731611	-1.13917247326995	0.425550041422787	0.676835754994839	0.774593376578848	-6.19000059303377	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930426L09Rik'>4930426L09Rik</a>
+Mdp1	-0.32178107969573	-0.848931461409027	-0.424206744137332	0.677792382558126	0.774910930359541	-6.17147301088386	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mdp1'>Mdp1</a>
+Mir5100	0.286079733326491	0.406104753719187	0.421137469236957	0.679980324136049	0.776133988892759	-6.12996948354496	18	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir5100'>Mir5100</a>
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+A230020J21Rik	-0.305089019444194	-0.452690836228738	-0.412631263938286	0.686059583143688	0.780372490447987	-6.13714270799574	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/A230020J21Rik'>A230020J21Rik</a>
+3110056K07Rik	0.321778367105555	-0.544811535499514	0.411774615698607	0.686673076608045	0.780372490447987	-6.15031511044177	9	<a href='http://www.genecards.org/index.php?path=/Search/keyword/3110056K07Rik'>3110056K07Rik</a>
+Mtf2	-0.351812353895571	-0.349382868103075	-0.407554645656379	0.689698567236507	0.783030910663537	-6.13041218971925	15	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mtf2'>Mtf2</a>
+BB123696	0.260421273935177	-1.13917247326995	0.404926598716839	0.691585522829203	0.784392725196939	-6.19874553892436	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/BB123696'>BB123696</a>
+Irf3	0.298133825217692	-1.07849411987367	0.396206543932785	0.697861753754696	0.790725184740922	-6.19569620036444	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Irf3'>Irf3</a>
+Mir18	-0.210024487848092	2.16031654478057	-0.393337083693313	0.699932088731125	0.792284239327593	-6.42958083480241	62	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir18'>Mir18</a>
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+9530052E02Rik	0.240241697353475	0.0356704882223265	0.376911575171499	0.71183041230099	0.803190169478922	-6.13775517192755	11	<a href='http://www.genecards.org/index.php?path=/Search/keyword/9530052E02Rik'>9530052E02Rik</a>
+F420014N23Rik	0.382817630756644	-0.117306762957363	0.375641100841847	0.712754019798555	0.803190169478922	-6.1456273280473	22	<a href='http://www.genecards.org/index.php?path=/Search/keyword/F420014N23Rik'>F420014N23Rik</a>
+Mir5129	-0.298231732945833	-0.452690836228738	-0.375183978987274	0.713086451956309	0.803190169478922	-6.15215700511858	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir5129'>Mir5129</a>
+Mir219-1	0.176264413953521	2.53670005639744	0.373534816743211	0.714286272130486	0.803748162229669	-6.50734777259605	90	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir219-1'>Mir219-1</a>
+Mir872	0.111217220149994	5.81048191699923	0.367908518024425	0.718385472265704	0.807166686595139	-7.01869601020665	859	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir872'>Mir872</a>
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+Snora78	-0.314719071095367	0.412167068430586	-0.365994199209784	0.719782263529738	0.807166686595139	-6.14978861932683	22	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora78'>Snora78</a>
+Orc4	0.297794064812266	-0.544811535499514	0.36548500236509	0.720153976296101	0.807166686595139	-6.16865012392074	9	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Orc4'>Orc4</a>
+Dnajc24	0.266599549793499	-0.558690449548107	0.354534559090483	0.728165394656301	0.815345157313876	-6.17320373339602	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnajc24'>Dnajc24</a>
+6720483E21Rik	0.289583824911831	-0.147092730894626	0.350649982201204	0.731015369891102	0.817733859848772	-6.15445263472245	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/6720483E21Rik'>6720483E21Rik</a>
+2310001K24Rik	-0.24591482502991	-1.03317285995058	-0.345230837127148	0.734998083052978	0.821383753930899	-6.22275270624135	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2310001K24Rik'>2310001K24Rik</a>
+Alg9	0.309421795900789	-0.676617508502311	0.343236944974775	0.736465460344019	0.822218287918323	-6.18698179945559	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Alg9'>Alg9</a>
+Snora81	-0.326932802874368	0.0115007762338971	-0.341850898914962	0.737486130537647	0.822552956933974	-6.14759719106399	22	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora81'>Snora81</a>
+BB283400	-0.279424707462514	-1.03317285995058	-0.340367255810976	0.738579239356336	0.822967687603104	-6.22446215814992	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/BB283400'>BB283400</a>
+Mir466d	0.248413625738754	-1.13917247326995	0.320824573653718	0.753031659736241	0.838252803667367	-6.2299984743374	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir466d'>Mir466d</a>
+Mir10a	0.0951038511256634	14.8586469353474	0.311728572155646	0.759791705201772	0.844953543504115	-7.67496459069947	435679	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10a'>Mir10a</a>
+Gm4890	-0.220857818504799	-1.24517208658932	-0.310290622719027	0.760862255053954	0.845320187942124	-6.25544681917468	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm4890'>Gm4890</a>
+6720401G13Rik	0.289187406074058	-1.11660094256472	0.307349482960207	0.763053506555847	0.84693001068115	-6.23186816538886	9	<a href='http://www.genecards.org/index.php?path=/Search/keyword/6720401G13Rik'>6720401G13Rik</a>
+5430402O13Rik	-0.217791204402388	-1.24517208658932	-0.304855090219651	0.764913568480844	0.847346001588973	-6.25716634200865	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/5430402O13Rik'>5430402O13Rik</a>
+Gm6297	-0.217791204402388	-1.24517208658932	-0.304855090219651	0.764913568480844	0.847346001588973	-6.25716634200865	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm6297'>Gm6297</a>
+Mir877	-0.206666454163989	1.57934953392826	-0.297694706970739	0.77026137051895	0.852442506073833	-6.34009404640788	45	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir877'>Mir877</a>
+Nol8	0.264698853020979	-0.386376496641391	0.293585635346632	0.7733357709552	0.855015614980507	-6.18259191534761	14	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Nol8'>Nol8</a>
+Snord58b	0.282727046691085	4.4176355838932	0.288358932677936	0.777252081328622	0.858513673568207	-6.87726871780058	394	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord58b'>Snord58b</a>
+Gm10785	-0.210547737676215	-1.07849411987367	-0.283356828799375	0.781005991911092	0.861118429107723	-6.24760352460985	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm10785'>Gm10785</a>
+1110019D14Rik	-0.222492569746086	-0.941052160679803	-0.283205434775104	0.781119696868092	0.861118429107723	-6.23175173996211	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1110019D14Rik'>1110019D14Rik</a>
+2010320M18Rik	0.206496077148502	-0.299891783561682	0.277852680238545	0.785143217405954	0.864718543494396	-6.18149015495467	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2010320M18Rik'>2010320M18Rik</a>
+Ccdc11	0.204900539151867	-1.13917247326995	0.274068094032085	0.787991843292579	0.866356392494407	-6.24428661528185	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Ccdc11'>Ccdc11</a>
+Zfp821	-0.202147777847892	-1.24517208658932	-0.273859508838947	0.788148935503238	0.866356392494407	-6.26639816102087	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Zfp821'>Zfp821</a>
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+5930430L01Rik	0.136225847581219	-0.214062543734675	0.119769549531324	0.906349281099135	0.941260828400483	-6.20916672317144	18	<a href='http://www.genecards.org/index.php?path=/Search/keyword/5930430L01Rik'>5930430L01Rik</a>
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+Mir362	-0.0544522631314578	3.35231486548691	-0.100710009948844	0.921193459854001	0.950345151621533	-6.73276860148804	169	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir362'>Mir362</a>
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+E230016M11Rik	-0.0696354231248524	-0.941052160679803	-0.0918911504840257	0.928072541539687	0.955713691242584	-6.26870805660384	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/E230016M11Rik'>E230016M11Rik</a>
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+Arhgap1	0.0966234721391633	-0.198705450261483	0.0890720608925429	0.930272835935954	0.956253428651282	-6.21090676133964	18	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Arhgap1'>Arhgap1</a>
+2610002J02Rik	-0.0573974454417385	-0.742931848089659	-0.0830721604333289	0.93495769271309	0.959921241425124	-6.24897822876549	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2610002J02Rik'>2610002J02Rik</a>
+4921531C22Rik	-0.0635851168193281	-0.941052160679803	-0.0822890634566592	0.93556934061789	0.959921241425124	-6.26957168238787	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4921531C22Rik'>4921531C22Rik</a>
+Srsf7	0.0705092857951172	-0.798864220211061	0.0812705943953252	0.936364891942299	0.959921241425124	-6.25432076732456	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Srsf7'>Srsf7</a>
+1700020I14Rik	0.0749473297339094	0.656660491848086	0.0792648453094152	0.937931837290533	0.960664476075851	-6.23371457269478	32	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1700020I14Rik'>1700020I14Rik</a>
+2210015D19Rik	0.0647102732837292	-1.23129317254072	0.0766096103443329	0.940006587546541	0.961787864403415	-6.29126291736405	5	<a href='http://www.genecards.org/index.php?path=/Search/keyword/2210015D19Rik'>2210015D19Rik</a>
+4732416N19Rik	0.0594207089292347	-0.239213430165402	0.0757037539631176	0.940714510669773	0.961787864403415	-6.21193843190686	11	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4732416N19Rik'>4732416N19Rik</a>
+Mir4660	0.0657262988065859	0.507946560272087	0.0713313665087823	0.944132233479521	0.964417975291077	-6.22141853049579	26	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir4660'>Mir4660</a>
+Mir5113	0.0484940420860439	-0.452690836228738	0.0682297423584027	0.946557346616918	0.966030351064315	-6.22526905240972	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir5113'>Mir5113</a>
+E530011L22Rik	-0.0404713843408522	-1.27661443246381	-0.0613724386888617	0.951920883212834	0.970284520587158	-6.29857782441741	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/E530011L22Rik'>E530011L22Rik</a>
+Gm15441	0.0426104096369733	1.51577639605449	0.0604630248332405	0.952632381396158	0.970284520587158	-6.37051029075163	43	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm15441'>Gm15441</a>
+Fam172a	0.0503754462959195	0.409161384184755	0.0596392630819191	0.953276904100091	0.970284520587158	-6.21618388102567	23	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Fam172a'>Fam172a</a>
+Rbm18	-0.0538668143348915	-0.299891783561682	-0.0557642901053547	0.956309184092742	0.972503368137093	-6.21475268708383	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Rbm18'>Rbm18</a>
+Gm12191	-0.0354587706805078	-0.880373807283523	-0.0497068478436261	0.961050697355324	0.975480839012736	-6.26527518040501	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm12191'>Gm12191</a>
+Rprl3	0.0408471478447264	-0.798864220211061	0.0488367850296659	0.961731876147215	0.975480839012736	-6.25649782741468	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Rprl3'>Rprl3</a>
+H19	-0.0415019911233814	-0.880373807283523	-0.0480992443304892	0.962309326654761	0.975480839012736	-6.26535636348749	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/H19'>H19</a>
+Ppifos	-0.045813233148843	-0.325698143245111	-0.047655434486338	0.962656813959983	0.975480839012736	-6.21600758126971	15	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Ppifos'>Ppifos</a>
+Mirlet7a-2	-0.0146726577509692	3.37472927372453	-0.0386745178686727	0.969690141624003	0.981735981892624	-6.74139737131634	158	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mirlet7a-2'>Mirlet7a-2</a>
+9530082P21Rik	-0.027891459987058	-1.27661443246381	-0.0346374807689275	0.972852600944678	0.983192929741255	-6.29990631175915	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/9530082P21Rik'>9530082P21Rik</a>
+Mir1196	-0.027891459987058	-1.27661443246381	-0.0346374807689275	0.972852600944678	0.983192929741255	-6.29990631175915	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1196'>Mir1196</a>
+Kcnk2	-0.0253403588431765	-0.835052547360434	-0.031369255395874	0.975413152136616	0.984908324414052	-6.26109829686273	7	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Kcnk2'>Kcnk2</a>
+A930011G23Rik	-0.0241809579465951	-0.00965077170076215	-0.0291709235913898	0.977135635463562	0.985775207837245	-6.2074206456237	12	<a href='http://www.genecards.org/index.php?path=/Search/keyword/A930011G23Rik'>A930011G23Rik</a>
+Mir3103	0.0180714470554271	-1.13917247326995	0.0259355368025229	0.979670906552206	0.987459809519494	-6.2920042186438	4	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3103'>Mir3103</a>
+Snora75	-0.0172327656019052	-0.590132795422603	-0.021476287065286	0.983165572405378	0.989793060148976	-6.23767380603265	10	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Snora75'>Snora75</a>
+4930414L22Rik	-0.0152743869054217	-0.484133182103234	-0.0207679670021376	0.983720710086713	0.989793060148976	-6.22874423282067	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/4930414L22Rik'>4930414L22Rik</a>
+Mipep	0.0164012673799433	-0.280376883322022	0.0179445082376201	0.985933647271923	0.991145631310365	-6.21618933242714	14	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mipep'>Mipep</a>
+Ippk	-0.0101933209515463	0.0857377294202925	-0.0128542290662295	0.989923536727642	0.99288598158411	-6.20831119150974	15	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Ippk'>Ippk</a>
+Mir598	-0.00787301950188535	1.52736379718861	-0.0127956250729132	0.989969473858512	0.99288598158411	-6.3747989571524	44	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir598'>Mir598</a>
+1500017E21Rik	0.0125149432592357	0.202348454937975	0.0124053255048405	0.990275413709656	0.99288598158411	-6.21004071500431	20	<a href='http://www.genecards.org/index.php?path=/Search/keyword/1500017E21Rik'>1500017E21Rik</a>
+Map1lc3a	0.00968300434227123	0.00717248334519302	0.0097742078067436	0.992337878036726	0.994080350166729	-6.20806203375241	21	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Map1lc3a'>Map1lc3a</a>
+Trappc13	-0.00465914834988075	-0.880373807283523	-0.00622703745231414	0.995118499154886	0.995991410119056	-6.26653097741332	6	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Trappc13'>Trappc13</a>
+Mir1966	-0.00246570556544304	-0.590132795422603	-0.00337044327478241	0.997357828291427	0.997357828291427	-6.23790561933129	8	<a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1966'>Mir1966</a>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/differential_count_models/test-data/gentestdata.sh	Wed Aug 07 01:58:28 2013 -0400
@@ -0,0 +1,9 @@
+#!/bin/bash
+# generate test data for rgGSEA
+# ross lazarus June 2013 
+# adjust gseajar_path !
+GSEAJAR_PATH=/home/rlazarus/galaxy-central/tool_dependency_dir/gsea_jar/2.0.12/fubar/rg_gsea_test/8e291f464aa0/jars/gsea2-2.0.12.jar
+python ../rgGSEA.py --input_tab "gsea_test_DGE.xls"  --adjpvalcol "5" --signcol "2" --idcol "1" --outhtml "gseatestout.html" --input_name "gsea_test" --setMax "500" --setMin "15" --nPerm "10" --plotTop "20" --gsea_jar "$GSEAJAR_PATH" --output_dir "gseatestout" --mode "Max_probe" 
+--title "GSEA test" --builtin_gmt "gseatestdata.gmt"
+
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/differential_count_models/test-data/test_bams2mx.xls	Wed Aug 07 01:58:28 2013 -0400
@@ -0,0 +1,3243 @@
+Contigname	11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam	11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam	11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam	11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam	11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam	11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam	11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam	11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam
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+Zfp207	5	0	2	0	0	9	1	2
+Zfp326	7	2	1	1	0	4	4	0
+Zfp389	0	0	0	0	0	0	0	0
+Zfp410	10	0	2	0	0	6	2	0
+Zfp414	1	0	0	0	0	4	0	0
+Zfp57	0	0	0	0	0	0	0	0
+Zfp572	0	0	0	0	0	0	0	0
+Zfp672	0	0	0	0	0	2	0	0
+Zfp783	0	0	0	0	0	0	0	0
+Zfp809	7	1	0	0	0	4	2	0
+Zfp821	0	0	0	2	2	0	0	0
+Zfp862	4	0	0	0	0	10	2	0
+Zim3	0	0	0	0	0	0	0	0
+Zmynd8	3	5	4	4	3	8	2	1
+Znf41-ps	0	0	0	0	0	0	0	0
+Zp4-ps	0	0	0	0	0	0	0	0
+Zscan4a	0	0	0	0	0	0	0	0
+Zxda	0	0	0	0	0	0	0	0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/differential_count_models/tool_dependencies.xml	Wed Aug 07 01:58:28 2013 -0400
@@ -0,0 +1,35 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="r3" version="3.0.1">
+        <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+    </package>package_ghostscript_9_07
+    <package name="ghostscript" version="9.07">
+        <repository changeset_revision="10222a7db54c" name="package_ghostscript_9_07" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+    </package>
+    <package name="graphicsmagick" version="1.3.18">
+        <repository changeset_revision="50d546dfd6b9" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+    </package>
+    <package name="biocbasics" version="2.12">
+        <install version="1.0"> 
+            <actions>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                        <package name="r3" version="3.0.1" />
+                    </repository>
+                </action>
+                <action type="make_directory">$INSTALL_DIR</action>
+                <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" &gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" &gt;&gt; $INSTALL_DIR/runme.R</action>
+                <action type="shell_command">echo "quit(save='no')" &gt;&gt; $INSTALL_DIR/runme.R</action>                
+                <action type="shell_command"> export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
+            </actions>
+        </install>
+        <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs
+        It's clunky but this is the most convenient way I could get anything installed into the package_r3
+        Note we use cran at fred hutch since no fastest mirror thingy
+       </readme>
+    </package>
+</tool_dependency>

--- a/rgedgeR/rgToolFactory.py	Sat Jul 27 22:28:00 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,605 +0,0 @@
-# rgToolFactory.py
-# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
-# 
-# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
-# 
-# all rights reserved
-# Licensed under the LGPL
-# suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
-#
-# july 2013
-# added ability to combine images and individual log files into html output
-# just make sure there's a log file foo.log and it will be output
-# together with all images named like "foo_*.pdf
-# otherwise old format for html
-#
-# January 2013
-# problem pointed out by Carlos Borroto
-# added escaping for <>$ - thought I did that ages ago...
-#
-# August 11 2012 
-# changed to use shell=False and cl as a sequence
-
-# This is a Galaxy tool factory for simple scripts in python, R or whatever ails ye.
-# It also serves as the wrapper for the new tool.
-# 
-# you paste and run your script
-# Only works for simple scripts that read one input from the history.
-# Optionally can write one new history dataset,
-# and optionally collect any number of outputs into links on an autogenerated HTML page.
-
-# DO NOT install on a public or important site - please.
-
-# installed generated tools are fine if the script is safe.
-# They just run normally and their user cannot do anything unusually insecure
-# but please, practice safe toolshed.
-# Read the fucking code before you install any tool 
-# especially this one
-
-# After you get the script working on some test data, you can
-# optionally generate a toolshed compatible gzip file
-# containing your script safely wrapped as an ordinary Galaxy script in your local toolshed for
-# safe and largely automated installation in a production Galaxy.
-
-# If you opt for an HTML output, you get all the script outputs arranged
-# as a single Html history item - all output files are linked, thumbnails for all the pdfs.
-# Ugly but really inexpensive.
-# 
-# Patches appreciated please. 
-#
-#
-# long route to June 2012 product
-# Behold the awesome power of Galaxy and the toolshed with the tool factory to bind them
-# derived from an integrated script model  
-# called rgBaseScriptWrapper.py
-# Note to the unwary:
-#   This tool allows arbitrary scripting on your Galaxy as the Galaxy user
-#   There is nothing stopping a malicious user doing whatever they choose
-#   Extremely dangerous!!
-#   Totally insecure. So, trusted users only
-#
-# preferred model is a developer using their throw away workstation instance - ie a private site.
-# no real risk. The universe_wsgi.ini admin_users string is checked - only admin users are permitted to run this tool.
-#
-
-import sys 
-import shutil 
-import subprocess 
-import os 
-import time 
-import tempfile 
-import optparse
-import tarfile
-import re
-import shutil
-import math
-
-progname = os.path.split(sys.argv[0])[1] 
-myversion = 'V000.2 June 2012' 
-verbose = False 
-debug = False
-toolFactoryURL = 'https://bitbucket.org/fubar/galaxytoolfactory'
-
-def timenow():
-    """return current time as a string
-    """
-    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
-
-html_escape_table = {
-     "&": "&amp;",
-     ">": "&gt;",
-     "<": "&lt;",
-     "$": "\$"
-     }
-
-def html_escape(text):
-     """Produce entities within text."""
-     return "".join(html_escape_table.get(c,c) for c in text)
-
-def cmd_exists(cmd):
-     return subprocess.call("type " + cmd, shell=True, 
-           stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0
-
-
-class ScriptRunner:
-    """class is a wrapper for an arbitrary script
-    """
-
-    def __init__(self,opts=None,treatbashSpecial=True):
-        """
-        cleanup inputs, setup some outputs
-        
-        """
-        self.useGM = cmd_exists('gm')
-        self.useIM = cmd_exists('convert')
-        self.useGS = cmd_exists('gs')
-        self.treatbashSpecial = treatbashSpecial
-        if opts.output_dir: # simplify for the tool tarball
-            os.chdir(opts.output_dir)
-        self.thumbformat = 'png'
-        self.opts = opts
-        self.toolname = re.sub('[^a-zA-Z0-9_]+', '', opts.tool_name) # a sanitizer now does this but..
-        self.toolid = self.toolname
-        self.myname = sys.argv[0] # get our name because we write ourselves out as a tool later
-        self.pyfile = self.myname # crude but efficient - the cruft won't hurt much
-        self.xmlfile = '%s.xml' % self.toolname
-        s = open(self.opts.script_path,'r').readlines()
-        s = [x.rstrip() for x in s] # remove pesky dos line endings if needed
-        self.script = '\n'.join(s)
-        fhandle,self.sfile = tempfile.mkstemp(prefix=self.toolname,suffix=".%s" % (opts.interpreter))
-        tscript = open(self.sfile,'w') # use self.sfile as script source for Popen
-        tscript.write(self.script)
-        tscript.close()
-        self.indentedScript = '\n'.join([' %s' % x for x in s]) # for restructured text in help
-        self.escapedScript = '\n'.join([html_escape(x) for x in s])
-        self.elog = os.path.join(self.opts.output_dir,"%s_error.log" % self.toolname)
-        if opts.output_dir: # may not want these complexities 
-            self.tlog = os.path.join(self.opts.output_dir,"%s_runner.log" % self.toolname)
-            art = '%s.%s' % (self.toolname,opts.interpreter)
-            artpath = os.path.join(self.opts.output_dir,art) # need full path
-            artifact = open(artpath,'w') # use self.sfile as script source for Popen
-            artifact.write(self.script)
-            artifact.close()
-        self.cl = []
-        self.html = []
-        a = self.cl.append
-        a(opts.interpreter)
-        if self.treatbashSpecial and opts.interpreter in ['bash','sh']:
-            a(self.sfile)
-        else:
-            a('-') # stdin
-        a(opts.input_tab)
-        a(opts.output_tab)
-        self.outFormats = 'tabular' # TODO make this an option at tool generation time
-        self.inputFormats = 'tabular' # TODO make this an option at tool generation time
-        self.test1Input = '%s_test1_input.xls' % self.toolname
-        self.test1Output = '%s_test1_output.xls' % self.toolname
-        self.test1HTML = '%s_test1_output.html' % self.toolname
-
-    def makeXML(self):
-        """
-        Create a Galaxy xml tool wrapper for the new script as a string to write out
-        fixme - use templating or something less fugly than this example of what we produce
-
-        <tool id="reverse" name="reverse" version="0.01">
-            <description>a tabular file</description>
-            <command interpreter="python">
-            reverse.py --script_path "$runMe" --interpreter "python" 
-            --tool_name "reverse" --input_tab "$input1" --output_tab "$tab_file" 
-            </command>
-            <inputs>
-            <param name="input1"  type="data" format="tabular" label="Select a suitable input file from your history"/><param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="reverse"/>
-
-            </inputs>
-            <outputs>
-            <data format="tabular" name="tab_file" label="${job_name}"/>
-
-            </outputs>
-            <help>
-            
-**What it Does**
-
-Reverse the columns in a tabular file
-
-            </help>
-            <configfiles>
-            <configfile name="runMe">
-            
-# reverse order of columns in a tabular file
-import sys
-inp = sys.argv[1]
-outp = sys.argv[2]
-i = open(inp,'r')
-o = open(outp,'w')
-for row in i:
-     rs = row.rstrip().split('\t')
-     rs.reverse()
-     o.write('\t'.join(rs))
-     o.write('\n')
-i.close()
-o.close()
- 
-
-            </configfile>
-            </configfiles>
-            </tool>
-        
-        """ 
-        newXML="""<tool id="%(toolid)s" name="%(toolname)s" version="%(tool_version)s">
-            %(tooldesc)s
-            %(command)s
-            <inputs>
-            %(inputs)s
-            </inputs>
-            <outputs>
-            %(outputs)s
-            </outputs>
-            <configfiles>
-            <configfile name="runMe">
-            %(script)s
-            </configfile>
-            </configfiles>
-            %(tooltests)s
-            <help>
-            %(help)s
-            </help>
-            </tool>""" # needs a dict with toolname, toolid, interpreter, scriptname, command, inputs as a multi line string ready to write, outputs ditto, help ditto
-               
-        newCommand="""<command interpreter="python">
-            %(toolname)s.py --script_path "$runMe" --interpreter "%(interpreter)s" 
-            --tool_name "%(toolname)s" %(command_inputs)s %(command_outputs)s 
-            </command>""" # may NOT be an input or htmlout
-        tooltestsTabOnly = """<tests><test>
-        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
-        <param name="job_name" value="test1"/>
-        <param name="runMe" value="$runMe"/>
-        <output name="tab_file" file="%(test1Output)s" ftype="tabular"/>
-        </test></tests>"""
-        tooltestsHTMLOnly = """<tests><test>
-        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
-        <param name="job_name" value="test1"/>
-        <param name="runMe" value="$runMe"/>
-        <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="5"/>
-        </test></tests>"""
-        tooltestsBoth = """<tests><test>
-        <param name="input1" value="%(test1Input)s" ftype="tabular"/>
-        <param name="job_name" value="test1"/>
-        <param name="runMe" value="$runMe"/>
-        <output name="tab_file" file="%(test1Output)s" ftype="tabular" />
-        <output name="html_file" file="%(test1HTML)s" ftype="html" lines_diff="10"/>
-        </test></tests>"""
-        xdict = {}
-        xdict['tool_version'] = self.opts.tool_version
-        xdict['test1Input'] = self.test1Input
-        xdict['test1HTML'] = self.test1HTML
-        xdict['test1Output'] = self.test1Output   
-        if self.opts.make_HTML and self.opts.output_tab <> 'None':
-            xdict['tooltests'] = tooltestsBoth % xdict
-        elif self.opts.make_HTML:
-            xdict['tooltests'] = tooltestsHTMLOnly % xdict
-        else:
-            xdict['tooltests'] = tooltestsTabOnly % xdict
-        xdict['script'] = self.escapedScript 
-        # configfile is least painful way to embed script to avoid external dependencies
-        # but requires escaping of <, > and $ to avoid Mako parsing
-        if self.opts.help_text:
-            xdict['help'] = open(self.opts.help_text,'r').read()
-        else:
-            xdict['help'] = 'Please ask the tool author for help as none was supplied at tool generation'
-        coda = ['**Script**','Pressing execute will run the following code over your input file and generate some outputs in your history::']
-        coda.append(self.indentedScript)
-        coda.append('**Attribution** This Galaxy tool was created by %s at %s\nusing the Galaxy Tool Factory.' % (self.opts.user_email,timenow()))
-        coda.append('See %s for details of that project' % (toolFactoryURL))
-        coda.append('Please cite: Creating re-usable tools from scripts: The Galaxy Tool Factory. Ross Lazarus; Antony Kaspi; Mark Ziemann; The Galaxy Team. ')
-        coda.append('Bioinformatics 2012; doi: 10.1093/bioinformatics/bts573')
-        xdict['help'] = '%s\n%s' % (xdict['help'],'\n'.join(coda))
-        if self.opts.tool_desc:
-            xdict['tooldesc'] = '<description>%s</description>' % self.opts.tool_desc
-        else:
-            xdict['tooldesc'] = ''
-        xdict['command_outputs'] = '' 
-        xdict['outputs'] = '' 
-        if self.opts.input_tab <> 'None':
-            xdict['command_inputs'] = '--input_tab "$input1" ' # the space may matter a lot if we append something
-            xdict['inputs'] = '<param name="input1"  type="data" format="%s" label="Select a suitable input file from your history"/> \n' % self.inputFormats
-        else:
-            xdict['command_inputs'] = '' # assume no input - eg a random data generator       
-            xdict['inputs'] = ''
-        xdict['inputs'] += '<param name="job_name" type="text" label="Supply a name for the outputs to remind you what they contain" value="%s"/> \n' % self.toolname
-        xdict['toolname'] = self.toolname
-        xdict['toolid'] = self.toolid
-        xdict['interpreter'] = self.opts.interpreter
-        xdict['scriptname'] = self.sfile
-        if self.opts.make_HTML:
-            xdict['command_outputs'] += ' --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" '
-            xdict['outputs'] +=  ' <data format="html" name="html_file" label="${job_name}.html"/>\n'
-        if self.opts.output_tab <> 'None':
-            xdict['command_outputs'] += ' --output_tab "$tab_file"'
-            xdict['outputs'] += ' <data format="%s" name="tab_file" label="${job_name}"/>\n' % self.outFormats
-        xdict['command'] = newCommand % xdict
-        xmls = newXML % xdict
-        xf = open(self.xmlfile,'w')
-        xf.write(xmls)
-        xf.write('\n')
-        xf.close()
-        # ready for the tarball
-
-
-    def makeTooltar(self):
-        """
-        a tool is a gz tarball with eg
-        /toolname/tool.xml /toolname/tool.py /toolname/test-data/test1_in.foo ...
-        """
-        retval = self.run()
-        if retval:
-            print >> sys.stderr,'## Run failed. Cannot build yet. Please fix and retry'
-            sys.exit(1)
-        self.makeXML()
-        tdir = self.toolname
-        os.mkdir(tdir)
-        if self.opts.input_tab <> 'None': # no reproducible test otherwise? TODO: maybe..
-            testdir = os.path.join(tdir,'test-data')
-            os.mkdir(testdir) # make tests directory
-            shutil.copyfile(self.opts.input_tab,os.path.join(testdir,self.test1Input))
-            if self.opts.output_tab <> 'None':
-                shutil.copyfile(self.opts.output_tab,os.path.join(testdir,self.test1Output))
-            if self.opts.make_HTML:
-                shutil.copyfile(self.opts.output_html,os.path.join(testdir,self.test1HTML))
-            if self.opts.output_dir:
-                shutil.copyfile(self.tlog,os.path.join(testdir,'test1_out.log'))
-        op = '%s.py' % self.toolname # new name
-        outpiname = os.path.join(tdir,op) # path for the tool tarball
-        pyin = os.path.basename(self.pyfile) # our name - we rewrite ourselves (TM)
-        notes = ['# %s - a self annotated version of %s generated by running %s\n' % (op,pyin,pyin),]
-        notes.append('# to make a new Galaxy tool called %s\n' % self.toolname)
-        notes.append('# User %s at %s\n' % (self.opts.user_email,timenow()))
-        pi = open(self.pyfile,'r').readlines() # our code becomes new tool wrapper (!) - first Galaxy worm
-        notes += pi
-        outpi = open(outpiname,'w')
-        outpi.write(''.join(notes))
-        outpi.write('\n')
-        outpi.close()
-        stname = os.path.join(tdir,self.sfile)
-        if not os.path.exists(stname):
-            shutil.copyfile(self.sfile, stname)
-        xtname = os.path.join(tdir,self.xmlfile)
-        if not os.path.exists(xtname):
-            shutil.copyfile(self.xmlfile,xtname)
-        tarpath = "%s.gz" % self.toolname
-        tar = tarfile.open(tarpath, "w:gz")
-        tar.add(tdir,arcname=self.toolname)
-        tar.close()
-        shutil.copyfile(tarpath,self.opts.new_tool)
-        shutil.rmtree(tdir)
-        ## TODO: replace with optional direct upload to local toolshed?
-        return retval
-
-
-    def compressPDF(self,inpdf=None,thumbformat='png'):
-        """need absolute path to pdf
-        """
-        assert os.path.isfile(inpdf), "## Input %s supplied to %s compressPDF not found" % (inpdf,self.myName)
-        hf,hlog = tempfile.mkstemp(suffix="%s.log" % self.toolname)
-        sto = open(hlog,'w')
-        outpdf = '%s_compressed' % inpdf
-        cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dBATCH","-dPDFSETTINGS=/printer", "-sOutputFile=%s" % outpdf,inpdf]
-        x = subprocess.Popen(cl,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
-        retval1 = x.wait()
-        if retval1 == 0:
-            os.unlink(inpdf)
-            shutil.move(outpdf,inpdf)
-        outpng = '%s.%s' % (os.path.splitext(inpdf)[0],thumbformat)
-        if self.useGM:        
-            cl2 = ['gm convert', inpdf, outpng]
-        else: # assume imagemagick
-            cl2 = ['convert', inpdf, outpng]
-        x = subprocess.Popen(cl2,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
-        retval2 = x.wait()
-        sto.close()
-        retval = retval1 or retval2
-        return retval
-
-
-    def getfSize(self,fpath,outpath):
-        """
-        format a nice file size string
-        """
-        size = ''
-        fp = os.path.join(outpath,fpath)
-        if os.path.isfile(fp):
-            size = '0 B'
-            n = float(os.path.getsize(fp))
-            if n > 2**20:
-                size = '%1.1f MB' % (n/2**20)
-            elif n > 2**10:
-                size = '%1.1f KB' % (n/2**10)
-            elif n > 0:
-                size = '%d B' % (int(n))
-        return size
-
-    def makeHtml(self):
-        """ Create an HTML file content to list all the artifacts found in the output_dir
-        """
-
-        galhtmlprefix = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> 
-        <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> 
-        <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> 
-        <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> 
-        <title></title> 
-        <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> 
-        </head> 
-        <body> 
-        <div class="toolFormBody"> 
-        """ 
-        galhtmlattr = """<hr/><div class="infomessage">This tool (%s) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>""" 
-        galhtmlpostfix = """</div></body></html>\n"""
-
-        flist = os.listdir(self.opts.output_dir)
-        flist = [x for x in flist if x <> 'Rplots.pdf']
-        flist.sort()
-        html = []
-        html.append(galhtmlprefix % progname)
-        html.append('<div class="infomessage">Galaxy Tool "%s" run at %s</div><br/>' % (self.toolname,timenow()))
-        fhtml = []
-        if len(flist) > 0:
-            logfiles = [x for x in flist if x.lower().endswith('.log')] # log file names determine sections
-            logfiles.sort()
-            logfiles = [x for x in logfiles if os.path.abspath(x) <> os.path.abspath(self.tlog)]
-            logfiles.append(os.path.abspath(self.tlog)) # make it the last one
-            pdflist = []
-            npdf = len([x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'])
-            for rownum,fname in enumerate(flist):
-                dname,e = os.path.splitext(fname)
-                sfsize = self.getfSize(fname,self.opts.output_dir)
-                if e.lower() == '.pdf' : # compress and make a thumbnail
-                    thumb = '%s.%s' % (dname,self.thumbformat)
-                    pdff = os.path.join(self.opts.output_dir,fname)
-                    retval = self.compressPDF(inpdf=pdff,thumbformat=self.thumbformat)
-                    if retval == 0:
-                        pdflist.append((fname,thumb))
-                if (rownum+1) % 2 == 0:
-                    fhtml.append('<tr class="odd_row"><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
-                else:
-                    fhtml.append('<tr><td><a href="%s">%s</a></td><td>%s</td></tr>' % (fname,fname,sfsize))
-            for logfname in logfiles: # expect at least tlog - if more
-                if os.path.abspath(logfname) == os.path.abspath(self.tlog): # handled later
-                    sectionname = 'All tool run'
-                    if (len(logfiles) > 1):
-                        sectionname = 'Other'
-                    ourpdfs = pdflist
-                else:
-                    realname = os.path.basename(logfname)
-                    sectionname = os.path.splitext(realname)[0].split('_')[0] # break in case _ added to log
-                    ourpdfs = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] == sectionname]
-                    pdflist = [x for x in pdflist if os.path.basename(x[0]).split('_')[0] <> sectionname] # remove
-                nacross = 1
-                npdf = len(ourpdfs)
-
-                if npdf > 0:
-                    nacross = math.sqrt(npdf) ## int(round(math.log(npdf,2)))
-                    if int(nacross)**2 != npdf:
-                        nacross += 1
-                    nacross = int(nacross)
-                    width = min(400,int(1200/nacross))
-                    html.append('<div class="toolFormTitle">%s images and outputs</div>' % sectionname)
-                    html.append('(Click on a thumbnail image to download the corresponding original PDF image)<br/>')
-                    ntogo = nacross # counter for table row padding with empty cells
-                    html.append('<div><table class="simple" cellpadding="2" cellspacing="2">\n<tr>')
-                    for i,paths in enumerate(ourpdfs): 
-                        fname,thumb = paths
-                        s= """<td><a href="%s"><img src="%s" title="Click to download a PDF of %s" hspace="5" width="%d" 
-                           alt="Image called %s"/></a></td>\n""" % (fname,thumb,fname,width,fname)
-                        if ((i+1) % nacross == 0):
-                            s += '</tr>\n'
-                            ntogo = 0
-                            if i < (npdf - 1): # more to come
-                               s += '<tr>'
-                               ntogo = nacross
-                        else:
-                            ntogo -= 1
-                        html.append(s)
-                    if html[-1].strip().endswith('</tr>'):
-                        html.append('</table></div>\n')
-                    else:
-                        if ntogo > 0: # pad
-                           html.append('<td>&nbsp;</td>'*ntogo)
-                        html.append('</tr></table></div>\n')
-                logt = open(logfname,'r').readlines()
-                logtext = [x for x in logt if x.strip() > '']
-                html.append('<div class="toolFormTitle">%s log output</div>' % sectionname)
-                if len(logtext) > 1:
-                    html.append('\n<pre>\n')
-                    html += logtext
-                    html.append('\n</pre>\n')
-                else:
-                    html.append('%s is empty<br/>' % logfname)
-        if len(fhtml) > 0:
-           fhtml.insert(0,'<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>\n')
-           fhtml.append('</table></div><br/>')
-           html.append('<div class="toolFormTitle">All output files available for downloading</div>\n')
-           html += fhtml # add all non-pdf files to the end of the display
-        else:
-            html.append('<div class="warningmessagelarge">### Error - %s returned no files - please confirm that parameters are sane</div>' % self.opts.interpreter)
-        html.append(galhtmlpostfix)
-        htmlf = file(self.opts.output_html,'w')
-        htmlf.write('\n'.join(html))
-        htmlf.write('\n')
-        htmlf.close()
-        self.html = html
-
-
-    def run(self):
-        """
-        scripts must be small enough not to fill the pipe!
-        """
-        if self.treatbashSpecial and self.opts.interpreter in ['bash','sh']:
-          retval = self.runBash()
-        else:
-            if self.opts.output_dir:
-                ste = open(self.elog,'w')
-                sto = open(self.tlog,'w')
-                sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
-                sto.flush()
-                p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
-            else:
-                p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
-            p.stdin.write(self.script)
-            p.stdin.close()
-            retval = p.wait()
-            if self.opts.output_dir:
-                sto.close()
-                ste.close()
-                err = open(self.elog,'r').readlines()
-                if retval <> 0 and err: # problem
-                    print >> sys.stderr,err
-            if self.opts.make_HTML:
-                self.makeHtml()
-        return retval
-
-    def runBash(self):
-        """
-        cannot use - for bash so use self.sfile
-        """
-        if self.opts.output_dir:
-            s = '## Toolfactory generated command line = %s\n' % ' '.join(self.cl)
-            sto = open(self.tlog,'w')
-            sto.write(s)
-            sto.flush()
-            p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
-        else:
-            p = subprocess.Popen(self.cl,shell=False)            
-        retval = p.wait()
-        if self.opts.output_dir:
-            sto.close()
-        if self.opts.make_HTML:
-            self.makeHtml()
-        return retval
-  
-
-def main():
-    u = """
-    This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
-    <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
-    </command>
-    """
-    op = optparse.OptionParser()
-    a = op.add_option
-    a('--script_path',default=None)
-    a('--tool_name',default=None)
-    a('--interpreter',default=None)
-    a('--output_dir',default=None)
-    a('--output_html',default=None)
-    a('--input_tab',default="None")
-    a('--output_tab',default="None")
-    a('--user_email',default='Unknown')
-    a('--bad_user',default=None)
-    a('--make_Tool',default=None)
-    a('--make_HTML',default=None)
-    a('--help_text',default=None)
-    a('--tool_desc',default=None)
-    a('--new_tool',default=None)
-    a('--tool_version',default=None)
-    opts, args = op.parse_args()
-    assert not opts.bad_user,'UNAUTHORISED: %s is NOT authorized to use this tool until Galaxy admin adds %s to admin_users in universe_wsgi.ini' % (opts.bad_user,opts.bad_user)
-    assert opts.tool_name,'## Tool Factory expects a tool name - eg --tool_name=DESeq'
-    assert opts.interpreter,'## Tool Factory wrapper expects an interpreter - eg --interpreter=Rscript'
-    assert os.path.isfile(opts.script_path),'## Tool Factory wrapper expects a script path - eg --script_path=foo.R'
-    if opts.output_dir:
-        try:
-            os.makedirs(opts.output_dir)
-        except:
-            pass
-    r = ScriptRunner(opts)
-    if opts.make_Tool:
-        retcode = r.makeTooltar()
-    else:
-        retcode = r.run()
-    os.unlink(r.sfile)
-    if retcode:
-        sys.exit(retcode) # indicate failure to job runner
-
-
-if __name__ == "__main__":
-    main()
-
-

--- a/rgedgeR/rgedgeRpaired.xml	Sat Jul 27 22:28:00 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,933 +0,0 @@
-<tool id="rgDifferentialCount" name="Differential_Count" version="0.20">
-  <description>models using BioConductor packages</description>
-  <requirements>
-      <requirement type="package" version="2.12">biocbasics</requirement>
-      <requirement type="package" version="3.0.1">r3</requirement>
-      <requirement type="package" version="1.3.18">graphicsmagick</requirement>
-      <requirement type="package" version="9.07">ghostscript</requirement>
-  </requirements>
-  
-  <command interpreter="python">
-     rgToolFactory.py --script_path "$runme" --interpreter "Rscript" --tool_name "DifferentialCounts" 
-    --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
-  </command>
-  <inputs>
-    <param name="input1"  type="data" format="tabular" label="Select an input matrix - rows are contigs, columns are counts for each sample"
-       help="Use the HTSeq based count matrix preparation tool to create these matrices from BAM/SAM files and a GTF file of genomic features"/>
-    <param name="title" type="text" value="Differential Counts" size="80" label="Title for job outputs" 
-           help="Supply a meaningful name here to remind you what the outputs contain">
-      <sanitizer invalid_char="">
-        <valid initial="string.letters,string.digits"><add value="_" /> </valid>
-      </sanitizer>
-    </param>
-    <param name="treatment_name" type="text" value="Treatment" size="50" label="Treatment Name"/>
-    <param name="Treat_cols" label="Select columns containing treatment." type="data_column" data_ref="input1" numerical="True" 
-         multiple="true" use_header_names="true" size="120" display="checkboxes">
-        <validator type="no_options" message="Please select at least one column."/>
-    </param>
-    <param name="control_name" type="text" value="Control" size="50" label="Control Name"/>
-    <param name="Control_cols" label="Select columns containing control." type="data_column" data_ref="input1" numerical="True" 
-         multiple="true" use_header_names="true" size="120" display="checkboxes" optional="true">
-    </param>
-    <param name="subjectids" type="text" optional="true" size="120" value = ""
-       label="IF SUBJECTS NOT ALL INDEPENDENT! Enter integers to indicate sample pairing for every column in input"
-       help="Leave blank if no pairing, but eg if data from sample id A99 is in columns 2,4 and id C21 is in 3,5 then enter '1,2,1,2'">
-      <sanitizer>
-        <valid initial="string.digits"><add value="," /> </valid>
-      </sanitizer>
-    </param>
-    <param name="fQ" type="float" value="0.3" size="5" label="Non-differential contig count quantile threshold - zero to analyze all non-zero read count contigs"
-     help="May be a good or a bad idea depending on the biology and the question. EG 0.3 = sparsest 30% of contigs with at least one read are removed before analysis"/>
-    <param name="useNDF" type="boolean" truevalue="T" falsevalue="F" checked="false" size="1" 
-              label="Non differential filter - remove contigs below a threshold (1 per million) for half or more samples"
-     help="May be a good or a bad idea depending on the biology and the question. This was the old default. Quantile based is available as an alternative"/>
-
-    <conditional name="edgeR">
-    <param name="doedgeR" type="select" 
-       label="Run this model using edgeR"
-       help="edgeR uses a negative binomial model and seems to be powerful, even with few replicates">
-      <option value="F">Do not run edgeR</option>
-      <option value="T" selected="true">Run edgeR</option>
-     </param>
-     <when value="T">
-      <param name="edgeR_priordf" type="integer" value="20" size="3" 
-       label="prior.df for tagwise dispersion - lower value = more emphasis on each tag's variance. Replaces prior.n  and prior.df = prior.n * residual.df"
-       help="0 = Use edgeR default. Use a small value to 'smooth' small samples. See edgeR docs and note below"/>
-     </when>
-     <when value="F"> </when>
-    </conditional>
-    <conditional name="DESeq2">
-    <param name="doDESeq2" type="select" 
-       label="Run the same model with DESeq2 and compare findings"
-       help="DESeq2 is an update to the DESeq package. It uses different assumptions and methods to edgeR">
-      <option value="F" selected="true">Do not run DESeq2</option>
-      <option value="T">Run DESeq2</option>
-     </param>
-     <when value="T">
-         <param name="DESeq_fitType" type="select">
-            <option value="parametric" selected="true">Parametric (default) fit for dispersions</option>
-            <option value="local">Local fit - this will automagically be used if parametric fit fails</option>
-            <option value="mean">Mean dispersion fit- use this if you really understand what you're doing - read the fine manual linked below in the documentation</option>
-         </param> 
-     </when>
-     <when value="F"> </when>
-    </conditional>
-    <param name="doVoom" type="select" 
-       label="Run the same model with Voom/limma and compare findings"
-       help="Voom uses counts per million and a precise transformation of variance so count data can be analysed using limma">
-      <option value="F" selected="true">Do not run VOOM</option>
-      <option value="T">Run VOOM</option>
-     </param>
-    <param name="fdrthresh" type="float" value="0.05" size="5" label="P value threshold for FDR filtering for amily wise error rate control"
-     help="Conventional default value of 0.05 recommended"/>
-    <param name="fdrtype" type="select" label="FDR (Type II error) control method" 
-         help="Use fdr or bh typically to control for the number of tests in a reliable way">
-            <option value="fdr" selected="true">fdr</option>
-            <option value="BH">Benjamini Hochberg</option>
-            <option value="BY">Benjamini Yukateli</option>
-            <option value="bonferroni">Bonferroni</option>
-            <option value="hochberg">Hochberg</option>
-            <option value="holm">Holm</option>
-            <option value="hommel">Hommel</option>
-            <option value="none">no control for multiple tests</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="tabular" name="out_edgeR" label="${title}_topTable_edgeR.xls">
-         <filter>edgeR['doedgeR'] == "T"</filter>
-    </data>
-    <data format="tabular" name="out_DESeq2" label="${title}_topTable_DESeq2.xls">
-         <filter>DESeq2['doDESeq2'] == "T"</filter>
-    </data>
-    <data format="tabular" name="out_VOOM" label="${title}_topTable_VOOM.xls">
-         <filter>doVoom == "T"</filter>
-    </data>
-    <data format="html" name="html_file" label="${title}.html"/>
-  </outputs>
- <stdio>
-     <exit_code range="4"   level="fatal"   description="Number of subject ids must match total number of samples in the input matrix" />
- </stdio>
- <tests>
-<test>
-<param name='input1' value='test_bams2mx.xls' ftype='tabular' />
- <param name='treatment_name' value='case' />
- <param name='title' value='edgeRtest' />
- <param name='useNDF' value='' />
- <param name='doedgeR' value='T' />
- <param name='doVoom' value='T' />
- <param name='doDESeq2' value='T' />
- <param name='fdrtype' value='fdr' />
- <param name='edgeR_priordf' value="8" />
- <param name='fdrthresh' value="0.05" />
- <param name='control_name' value='control' />
- <param name='subjectids' value='' />
-  <param name='Treat_cols' value='3,4,5,9' />
- <param name='Control_cols' value='2,6,7,8' />
- <output name='out_edgeR' file='edgeRtest1out.xls' compare='diff' />
- <output name='html_file' file='edgeRtest1out.html'  compare='diff' lines_diff='20' />
-</test>
-</tests>
-
-<configfiles>
-<configfile name="runme">
-<![CDATA[
-# 
-# edgeR.Rscript
-# updated npv 2011 for R 2.14.0 and edgeR 2.4.0 by ross
-# Performs DGE on a count table containing n replicates of two conditions
-#
-# Parameters
-#
-# 1 - Output Dir
-
-# Original edgeR code by: S.Lunke and A.Kaspi
-reallybig = log10(.Machine\$double.xmax)
-reallysmall = log10(.Machine\$double.xmin)
-library('stringr')
-library('gplots')
-library('edgeR')
-hmap2 = function(cmat,nsamp=100,outpdfname='heatmap2.pdf', TName='Treatment',group=NA,myTitle='title goes here')
-{
-# Perform clustering for significant pvalues after controlling FWER
-    samples = colnames(cmat)
-    gu = unique(group)
-    if (length(gu) == 2) {
-        col.map = function(g) {if (g==gu[1]) "#FF0000" else "#0000FF"}
-        pcols = unlist(lapply(group,col.map))        
-        } else {
-        colours = rainbow(length(gu),start=0,end=4/6)
-        pcols = colours[match(group,gu)]        }
-    gn = rownames(cmat)
-    dm = cmat[(! is.na(gn)),] 
-    # remove unlabelled hm rows
-    nprobes = nrow(dm)
-    # sub = paste('Showing',nprobes,'contigs ranked for evidence of differential abundance')
-    if (nprobes > nsamp) {
-      dm =dm[1:nsamp,]
-      #sub = paste('Showing',nsamp,'contigs ranked for evidence for differential abundance out of',nprobes,'total')
-    }
-    newcolnames = substr(colnames(dm),1,20)
-    colnames(dm) = newcolnames
-    pdf(outpdfname)
-    heatmap.2(dm,main=myTitle,ColSideColors=pcols,col=topo.colors(100),dendrogram="col",key=T,density.info='none',
-         Rowv=F,scale='row',trace='none',margins=c(8,8),cexRow=0.4,cexCol=0.5)
-    dev.off()
-}
-
-hmap = function(cmat,nmeans=4,outpdfname="heatMap.pdf",nsamp=250,TName='Treatment',group=NA,myTitle="Title goes here")
-{
-    # for 2 groups only was
-    #col.map = function(g) {if (g==TName) "#FF0000" else "#0000FF"}
-    #pcols = unlist(lapply(group,col.map))
-    gu = unique(group)
-    colours = rainbow(length(gu),start=0.3,end=0.6)
-    pcols = colours[match(group,gu)]
-    nrows = nrow(cmat)
-    mtitle = paste(myTitle,'Heatmap: n contigs =',nrows)
-    if (nrows > nsamp)  {
-               cmat = cmat[c(1:nsamp),]
-               mtitle = paste('Heatmap: Top ',nsamp,' DE contigs (of ',nrows,')',sep='')
-          }
-    newcolnames = substr(colnames(cmat),1,20)
-    colnames(cmat) = newcolnames
-    pdf(outpdfname)
-    heatmap(cmat,scale='row',main=mtitle,cexRow=0.3,cexCol=0.4,Rowv=NA,ColSideColors=pcols)
-    dev.off()
-}
-
-qqPlot = function(descr='qqplot',pvector, outpdf='qqplot.pdf',...)
-# stolen from https://gist.github.com/703512
-{
-    o = -log10(sort(pvector,decreasing=F))
-    e = -log10( 1:length(o)/length(o) )
-    o[o==-Inf] = reallysmall
-    o[o==Inf] = reallybig
-    maint = descr
-    pdf(outpdf)
-    plot(e,o,pch=19,cex=1, main=maint, ...,
-        xlab=expression(Expected~~-log[10](italic(p))),
-        ylab=expression(Observed~~-log[10](italic(p))),
-        xlim=c(0,max(e)), ylim=c(0,max(o)))
-    lines(e,e,col="red")
-    grid(col = "lightgray", lty = "dotted")
-    dev.off()
-}
-
-smearPlot = function(DGEList,deTags, outSmear, outMain)
-        {
-        pdf(outSmear)
-        plotSmear(DGEList,de.tags=deTags,main=outMain)
-        grid(col="lightgray", lty="dotted")
-        dev.off()
-        }
-        
-boxPlot = function(rawrs,cleanrs,maint,myTitle,pdfname)
-{   # 
-        nc = ncol(rawrs)
-        for (i in c(1:nc)) {rawrs[(rawrs[,i] < 0),i] = NA}
-        fullnames = colnames(rawrs)
-        newcolnames = substr(colnames(rawrs),1,20)
-        colnames(rawrs) = newcolnames
-        newcolnames = substr(colnames(cleanrs),1,20)
-        colnames(cleanrs) = newcolnames
-        defpar = par(no.readonly=T)
-        print.noquote('raw contig counts by sample:')
-        print.noquote(summary(rawrs))
-        print.noquote('normalised contig counts by sample:')
-        print.noquote(summary(cleanrs))
-        pdf(pdfname)
-        par(mfrow=c(1,2))
-        boxplot(rawrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('Raw:',maint))
-        grid(col="lightgray",lty="dotted")
-        boxplot(cleanrs,varwidth=T,notch=T,ylab='log contig count',col="maroon",las=3,cex.axis=0.35,main=paste('After ',maint))
-        grid(col="lightgray",lty="dotted")
-        dev.off()
-        pdfname = "sample_counts_histogram.pdf" 
-        nc = ncol(rawrs)
-        print.noquote(paste('Using ncol rawrs=',nc))
-        ncroot = round(sqrt(nc))
-        if (ncroot*ncroot < nc) { ncroot = ncroot + 1 }
-        m = c()
-        for (i in c(1:nc)) {
-              rhist = hist(rawrs[,i],breaks=100,plot=F)
-              m = append(m,max(rhist\$counts))
-             }
-        ymax = max(m)
-        pdf(pdfname)
-        par(mfrow=c(ncroot,ncroot))
-        for (i in c(1:nc)) {
-                 hist(rawrs[,i], main=paste("Contig logcount",i), xlab='log raw count', col="maroon", 
-                 breaks=100,sub=fullnames[i],cex=0.8,ylim=c(0,ymax))
-             }
-        dev.off()
-        par(defpar)
-      
-}
-
-cumPlot = function(rawrs,cleanrs,maint,myTitle)
-{   # updated to use ecdf
-        pdfname = "Filtering_rowsum_bar_charts.pdf"
-        defpar = par(no.readonly=T)
-        lrs = log(rawrs,10) 
-        lim = max(lrs)
-        pdf(pdfname)
-        par(mfrow=c(2,1))
-        hist(lrs,breaks=100,main=paste('Before:',maint),xlab="# Reads (log)",
-             ylab="Count",col="maroon",sub=myTitle, xlim=c(0,lim),las=1)
-        grid(col="lightgray", lty="dotted")
-        lrs = log(cleanrs,10) 
-        hist(lrs,breaks=100,main=paste('After:',maint),xlab="# Reads (log)",
-             ylab="Count",col="maroon",sub=myTitle,xlim=c(0,lim),las=1)
-        grid(col="lightgray", lty="dotted")
-        dev.off()
-        par(defpar)
-}
-
-cumPlot1 = function(rawrs,cleanrs,maint,myTitle)
-{   # updated to use ecdf
-        pdfname = paste(gsub(" ","", myTitle , fixed=TRUE),"RowsumCum.pdf",sep='_')
-        pdf(pdfname)
-        par(mfrow=c(2,1))
-        lastx = max(rawrs)
-        rawe = knots(ecdf(rawrs))
-        cleane = knots(ecdf(cleanrs))
-        cy = 1:length(cleane)/length(cleane)
-        ry = 1:length(rawe)/length(rawe)
-        plot(rawe,ry,type='l',main=paste('Before',maint),xlab="Log Contig Total Reads",
-             ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle)
-        grid(col="blue")
-        plot(cleane,cy,type='l',main=paste('After',maint),xlab="Log Contig Total Reads",
-             ylab="Cumulative proportion",col="maroon",log='x',xlim=c(1,lastx),sub=myTitle)
-        grid(col="blue")
-        dev.off()
-}
-
-
-
-doGSEA = function(y=NULL,design=NULL,histgmt="",
-                  bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
-                  ntest=0, myTitle="myTitle", outfname="GSEA.xls", minnin=5, maxnin=2000,fdrthresh=0.05,fdrtype="BH")
-{
-  sink('Camera.log')
-  genesets = c()
-  if (bigmt > "")
-  {
-    bigenesets = readLines(bigmt)
-    genesets = bigenesets
-  }
-  if (histgmt > "")
-  {
-    hgenesets = readLines(histgmt)
-    if (bigmt > "") {
-      genesets = rbind(genesets,hgenesets)
-    } else {
-      genesets = hgenesets
-    } # use only history if no bi
-  }
-  print.noquote(paste("@@@read",length(genesets), 'genesets from',histgmt,bigmt))
-  genesets = strsplit(genesets,'\t') # tabular. genesetid\tURLorwhatever\tgene_1\t..\tgene_n
-  outf = outfname
-  head=paste(myTitle,'edgeR GSEA')
-  write(head,file=outfname,append=F)
-  ntest=length(genesets)
-  urownames = toupper(rownames(y))
-  upcam = c()
-  downcam = c()
-  for (i in 1:ntest) {
-    gs = unlist(genesets[i])
-    g = gs[1] # geneset_id
-    u = gs[2]
-    if (u > "") { u = paste("<a href=\'",u,"\'>",u,"</a>",sep="") }
-    glist = gs[3:length(gs)] # member gene symbols
-    glist = toupper(glist)
-    inglist = urownames %in% glist
-    nin = sum(inglist)
-    if ((nin > minnin) && (nin < maxnin)) {
-      ### print(paste('@@found',sum(inglist),'genes in glist'))
-      camres = camera(y=y,index=inglist,design=design)
-      if (! is.null(camres)) {
-      rownames(camres) = g # gene set name
-      camres = cbind(GeneSet=g,URL=u,camres)
-      if (camres\$Direction == "Up") 
-        {
-        upcam = rbind(upcam,camres) } else {
-          downcam = rbind(downcam,camres)
-        }
-      }
-   }
-  }
-  uscam = upcam[order(upcam\$PValue),]
-  unadjp = uscam\$PValue
-  uscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
-  nup = max(10,sum((uscam\$adjPValue < fdrthresh)))
-  dscam = downcam[order(downcam\$PValue),]
-  unadjp = dscam\$PValue
-  dscam\$adjPValue = p.adjust(unadjp,method=fdrtype)
-  ndown = max(10,sum((dscam\$adjPValue < fdrthresh)))
-  write.table(uscam,file=paste('camera_up',outfname,sep='_'),quote=F,sep='\t',row.names=F)
-  write.table(dscam,file=paste('camera_down',outfname,sep='_'),quote=F,sep='\t',row.names=F)
-  print.noquote(paste('@@@@@ Camera up top',nup,'gene sets:'))
-  write.table(head(uscam,nup),file="",quote=F,sep='\t',row.names=F)
-  print.noquote(paste('@@@@@ Camera down top',ndown,'gene sets:'))
-  write.table(head(dscam,ndown),file="",quote=F,sep='\t',row.names=F)
-  sink()
-}
-
-
-
-edgeIt = function (Count_Matrix=c(),group=c(),out_edgeR=F,out_VOOM=F,out_DESeq2=F,fdrtype='fdr',priordf=5, 
-        fdrthresh=0.05,outputdir='.', myTitle='Differential Counts',libSize=c(),useNDF=F,
-        filterquantile=0.2, subjects=c(),mydesign=NULL,
-        doDESeq2=T,doVoom=T,doCamera=T,doedgeR=T,org='hg19',
-        histgmt="", bigmt="/data/genomes/gsea/3.1/Abetterchoice_nocgp_c2_c3_c5_symbols_all.gmt",
-        doCook=F,DESeq_fitType="parameteric") 
-{
-  # Error handling
-  if (length(unique(group))!=2){
-    print("Number of conditions identified in experiment does not equal 2")
-    q()
-    }
-  require(edgeR)
-  options(width = 512) 
-  mt = paste(unlist(strsplit(myTitle,'_')),collapse=" ")
-  allN = nrow(Count_Matrix)
-  nscut = round(ncol(Count_Matrix)/2)
-  colTotmillionreads = colSums(Count_Matrix)/1e6
-  counts.dataframe = as.data.frame(c()) 
-  rawrs = rowSums(Count_Matrix)
-  nonzerod = Count_Matrix[(rawrs > 0),] # remove all zero count genes
-  nzN = nrow(nonzerod)
-  nzrs = rowSums(nonzerod)
-  zN = allN - nzN
-  print('# Quantiles for non-zero row counts:',quote=F)
-  print(quantile(nzrs,probs=seq(0,1,0.1)),quote=F)
-  if (useNDF == T)
-  {
-    gt1rpin3 = rowSums(Count_Matrix/expandAsMatrix(colTotmillionreads,dim(Count_Matrix)) >= 1) >= nscut
-    lo = colSums(Count_Matrix[!gt1rpin3,])
-    workCM = Count_Matrix[gt1rpin3,]
-    cleanrs = rowSums(workCM)
-    cleanN = length(cleanrs)
-    meth = paste( "After removing",length(lo),"contigs with fewer than ",nscut," sample read counts >= 1 per million, there are",sep="")
-    print(paste("Read",allN,"contigs. Removed",zN,"contigs with no reads.",meth,cleanN,"contigs"),quote=F)
-    maint = paste('Filter >=1/million reads in >=',nscut,'samples')
-  }   else {        
-    useme = (nzrs > quantile(nzrs,filterquantile))
-    workCM = nonzerod[useme,]
-    lo = colSums(nonzerod[!useme,])
-    cleanrs = rowSums(workCM)
-    cleanN = length(cleanrs)
-    meth = paste("After filtering at count quantile =",filterquantile,", there are",sep="")
-    print(paste('Read',allN,"contigs. Removed",zN,"with no reads.",meth,cleanN,"contigs"),quote=F)
-    maint = paste('Filter below',filterquantile,'quantile')
-  }
-  cumPlot(rawrs=rawrs,cleanrs=cleanrs,maint=maint,myTitle=myTitle)
-  allgenes = rownames(workCM)
-  reg = "^chr([0-9]+):([0-9]+)-([0-9]+)"
-  genecards="<a href=\'http://www.genecards.org/index.php?path=/Search/keyword/"
-  ucsc = paste("<a href=\'http://genome.ucsc.edu/cgi-bin/hgTracks?db=",org,sep='')
-  testreg = str_match(allgenes,reg)
-  if (sum(!is.na(testreg[,1]))/length(testreg[,1]) > 0.8) # is ucsc style string
-  {
-    print("@@ using ucsc substitution for urls")
-    contigurls = paste0(ucsc,"&amp;position=chr",testreg[,2],":",testreg[,3],"-",testreg[,4],"\'>",allgenes,"</a>")
-  } else {
-    print("@@ using genecards substitution for urls")
-    contigurls = paste0(genecards,allgenes,"\'>",allgenes,"</a>")
-  }
-  print.noquote("# urls")
-  print.noquote(head(contigurls))
-  print(paste("# Total low count contigs per sample = ",paste(lo,collapse=',')),quote=F) 
-  cmrowsums = rowSums(workCM)
-  TName=unique(group)[1]
-  CName=unique(group)[2]
-  if (is.null(mydesign)) {
-    if (length(subjects) == 0) 
-    {
-      mydesign = model.matrix(~group)
-    } 
-    else { 
-      subjf = factor(subjects)
-      mydesign = model.matrix(~subjf+group) # we block on subject so make group last to simplify finding it
-    }
-  } 
-  print.noquote(paste('Using samples:',paste(colnames(workCM),collapse=',')))
-  print.noquote('Using design matrix:')
-  print.noquote(mydesign)
-  if (doedgeR) {
-  sink('edgeR.log')
-  #### Setup DGEList object
-  DGEList = DGEList(counts=workCM, group = group)
-  DGEList = calcNormFactors(DGEList)
-
-  DGEList = estimateGLMCommonDisp(DGEList,mydesign)
-  comdisp = DGEList\$common.dispersion
-  DGEList = estimateGLMTrendedDisp(DGEList,mydesign)
-  if (edgeR_priordf > 0) {
-    print.noquote(paste("prior.df =",edgeR_priordf))
-    DGEList = estimateGLMTagwiseDisp(DGEList,mydesign,prior.df = edgeR_priordf)
-  } else {
-    DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
-  }
-  DGLM = glmFit(DGEList,design=mydesign)
-  DE = glmLRT(DGLM,coef=ncol(DGLM\$design)) # always last one - subject is first if needed
-  efflib = DGEList\$samples\$lib.size*DGEList\$samples\$norm.factors
-  normData = (1e+06*DGEList\$counts/efflib)
-  uoutput = cbind( 
-    Name=as.character(rownames(DGEList\$counts)),
-    DE\$table,
-    adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
-    Dispersion=DGEList\$tagwise.dispersion,totreads=cmrowsums,normData,
-    DGEList\$counts
-  )
-  soutput = uoutput[order(DE\$table\$PValue),] # sorted into p value order - for quick toptable
-  goodness = gof(DGLM, pcutoff=fdrthresh)
-  if (sum(goodness\$outlier) > 0) {
-    print.noquote('GLM outliers:')
-    print(paste(rownames(DGLM)[(goodness\$outlier)],collapse=','),quote=F)
-    } else { 
-      print('No GLM fit outlier genes found\n')
-    }
-  z = limma::zscoreGamma(goodness\$gof.statistic, shape=goodness\$df/2, scale=2)
-  pdf("edgeR_GoodnessofFit.pdf")
-  qq = qqnorm(z, panel.first=grid(), main="tagwise dispersion")
-  abline(0,1,lwd=3)
-  points(qq\$x[goodness\$outlier],qq\$y[goodness\$outlier], pch=16, col="maroon")
-  dev.off()
-  estpriorn = getPriorN(DGEList)
-  print(paste("Common Dispersion =",comdisp,"CV = ",sqrt(comdisp),"getPriorN = ",estpriorn),quote=F)
-  efflib = DGEList\$samples\$lib.size*DGEList\$samples\$norm.factors
-  normData = (1e+06*DGEList\$counts/efflib)
-  uniqueg = unique(group)
-  #### Plot MDS
-  sample_colors =  match(group,levels(group))
-  sampleTypes = levels(factor(group))
-  print.noquote(sampleTypes)
-  pdf("edgeR_MDSplot.pdf")
-  plotMDS.DGEList(DGEList,main=paste("edgeR MDS for",myTitle),cex=0.5,col=sample_colors,pch=sample_colors)
-  legend(x="topleft", legend = sampleTypes,col=c(1:length(sampleTypes)), pch=19)
-  grid(col="blue")
-  dev.off()
-  colnames(normData) = paste( colnames(normData),'N',sep="_")
-  print(paste('Raw sample read totals',paste(colSums(nonzerod,na.rm=T),collapse=',')))
-  nzd = data.frame(log(nonzerod + 1e-2,10))
-  boxPlot(rawrs=nzd,cleanrs=log(normData,10),maint='TMM Normalisation',myTitle=myTitle,pdfname="edgeR_raw_norm_counts_box.pdf")
-  write.table(soutput,file=out_edgeR, quote=FALSE, sep="\t",row.names=F)
-  tt = cbind( 
-    Name=as.character(rownames(DGEList\$counts)),
-    DE\$table,
-    adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
-    Dispersion=DGEList\$tagwise.dispersion,totreads=cmrowsums
-  )
-  print.noquote("# edgeR Top tags\n")
-  tt = cbind(tt,URL=contigurls) # add to end so table isn't laid out strangely
-  tt = tt[order(DE\$table\$PValue),] 
-  print.noquote(tt[1:50,])
-  deTags = rownames(uoutput[uoutput\$adj.p.value < fdrthresh,])
-  nsig = length(deTags)
-  print(paste('#',nsig,'tags significant at adj p=',fdrthresh),quote=F)
-  deColours = ifelse(deTags,'red','black')
-  pdf("edgeR_BCV_vs_abundance.pdf")
-  plotBCV(DGEList, cex=0.3, main="Biological CV vs abundance")
-  dev.off()
-  dg = DGEList[order(DE\$table\$PValue),]
-  #normData = (1e+06 * dg\$counts/expandAsMatrix(dg\$samples\$lib.size, dim(dg)))
-  efflib = dg\$samples\$lib.size*dg\$samples\$norm.factors
-  normData = (1e+06*dg\$counts/efflib)
-  outpdfname="edgeR_top_100_heatmap.pdf"
-  hmap2(normData,nsamp=100,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste('edgeR Heatmap',myTitle))
-  outSmear = "edgeR_smearplot.pdf"
-  outMain = paste("Smear Plot for ",TName,' Vs ',CName,' (FDR@',fdrthresh,' N = ',nsig,')',sep='')
-  smearPlot(DGEList=DGEList,deTags=deTags, outSmear=outSmear, outMain = outMain)
-  qqPlot(descr=paste(myTitle,'edgeR adj p QQ plot'),pvector=tt\$adj.p.value,outpdf='edgeR_qqplot.pdf')
-  norm.factor = DGEList\$samples\$norm.factors
-  topresults.edgeR = soutput[which(soutput\$adj.p.value < fdrthresh), ]
-  edgeRcountsindex = which(allgenes %in% rownames(topresults.edgeR))
-  edgeRcounts = rep(0, length(allgenes))
-  edgeRcounts[edgeRcountsindex] = 1  # Create venn diagram of hits
-  sink()
-  } ### doedgeR
-  if (doDESeq2 == T)
-  {
-    sink("DESeq2.log")
-    # DESeq2
-    require('DESeq2')
-    library('RColorBrewer')
-    pdata = data.frame(Name=colnames(workCM),Rx=group,row.names=colnames(workCM))        
-    deSEQds = DESeqDataSetFromMatrix(countData = workCM,  colData = pdata, design = formula(~ Rx))
-    #DESeq2 = DESeq(deSEQds,fitType='local',pAdjustMethod=fdrtype)
-    #rDESeq = results(DESeq2)
-    #newCountDataSet(workCM, group)
-    deSeqDatsizefac = estimateSizeFactors(deSEQds)
-    deSeqDatdisp = estimateDispersions(deSeqDatsizefac,fitType=DESeq_fitType)
-    resDESeq = nbinomWaldTest(deSeqDatdisp, pAdjustMethod=fdrtype)
-    rDESeq = as.data.frame(results(resDESeq))
-    rDESeq = cbind(Contig=rownames(workCM),rDESeq,NReads=cmrowsums,URL=contigurls)
-    srDESeq = rDESeq[order(rDESeq\$pvalue),]
-    qqPlot(descr=paste(myTitle,'DESeq2 adj p qq plot'),pvector=rDESeq\$padj,outpdf='DESeq2_qqplot.pdf')
-    cat("# DESeq top 50\n")
-    print.noquote(srDESeq[1:50,])
-    write.table(srDESeq,file=out_DESeq2, quote=FALSE, sep="\t",row.names=F)
-    topresults.DESeq = rDESeq[which(rDESeq\$padj < fdrthresh), ]
-    DESeqcountsindex = which(allgenes %in% rownames(topresults.DESeq))
-    DESeqcounts = rep(0, length(allgenes))
-    DESeqcounts[DESeqcountsindex] = 1
-    pdf("DESeq2_dispersion_estimates.pdf")
-    plotDispEsts(resDESeq)
-    dev.off()
-    ysmall = abs(min(rDESeq\$log2FoldChange))
-    ybig = abs(max(rDESeq\$log2FoldChange))
-    ylimit = min(4,ysmall,ybig)
-    pdf("DESeq2_MA_plot.pdf")
-    plotMA(resDESeq,main=paste(myTitle,"DESeq2 MA plot"),ylim=c(-ylimit,ylimit))
-    dev.off()
-    rlogres = rlogTransformation(resDESeq)
-    sampledists = dist( t( assay(rlogres) ) )
-    sdmat = as.matrix(sampledists)
-    pdf("DESeq2_sample_distance_plot.pdf")
-    heatmap.2(sdmat,trace="none",main=paste(myTitle,"DESeq2 sample distances"),
-         col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255))
-    dev.off()
-    sink()
-    result = try( (ppca = plotPCA( varianceStabilizingTransformation(deSeqDatdisp,blind=T), intgroup=c("Rx","Name")) ) )
-    if ("try-error" %in% class(result)) {
-         print.noquote('DESeq2 plotPCA failed.')
-         } else {
-         pdf("DESeq2_PCA_plot.pdf")
-         #### wtf - print? Seems needed to get this to work
-         print(ppca)
-         dev.off()
-        }
-  }
-
-  if (doVoom == T) {
-      sink('VOOM.log')
-      if (doedgeR == F) {
-         #### Setup DGEList object
-         DGEList = DGEList(counts=workCM, group = group)
-         DGEList = calcNormFactors(DGEList)
-         DGEList = estimateGLMCommonDisp(DGEList,mydesign)
-         DGEList = estimateGLMTrendedDisp(DGEList,mydesign)
-         DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
-         DGEList = estimateGLMTagwiseDisp(DGEList,mydesign)
-         norm.factor = DGEList\$samples\$norm.factors
-         }
-      pdf("VOOM_mean_variance_plot.pdf")
-      dat.voomed = voom(DGEList, mydesign, plot = TRUE, lib.size = colSums(workCM) * norm.factor)
-      dev.off()
-      # Use limma to fit data
-      fit = lmFit(dat.voomed, mydesign)
-      fit = eBayes(fit)
-      rvoom = topTable(fit, coef = length(colnames(mydesign)), adj = fdrtype, n = Inf, sort="none")
-      qqPlot(descr=paste(myTitle,'VOOM-limma adj p QQ plot'),pvector=rvoom\$adj.P.Val,outpdf='VOOM_qqplot.pdf')
-      rownames(rvoom) = rownames(workCM)
-      rvoom = cbind(rvoom,NReads=cmrowsums,URL=contigurls)
-      srvoom = rvoom[order(rvoom\$P.Value),]
-      cat("# VOOM top 50\n")
-      print(srvoom[1:50,])
-      write.table(srvoom,file=out_VOOM, quote=FALSE, sep="\t",row.names=F)
-      # Use an FDR cutoff to find interesting samples for edgeR, DESeq and voom/limma
-      topresults.voom = srvoom[which(rvoom\$adj.P.Val < fdrthresh), ]
-      voomcountsindex = which(allgenes %in% topresults.voom\$ID)
-      voomcounts = rep(0, length(allgenes))
-      voomcounts[voomcountsindex] = 1
-      sink()
-  }
-
-  if (doCamera) {
-  doGSEA(y=DGEList,design=mydesign,histgmt=histgmt,bigmt=bigmt,ntest=20,myTitle=myTitle,
-    outfname=paste(mt,"GSEA.xls",sep="_"),fdrthresh=fdrthresh,fdrtype=fdrtype)
-  }
-
-  if ((doDESeq2==T) || (doVoom==T) || (doedgeR==T)) {
-    if ((doVoom==T) && (doDESeq2==T) && (doedgeR==T)) {
-        vennmain = paste(mt,'Voom,edgeR and DESeq2 overlap at FDR=',fdrthresh)
-        counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts, 
-                                       VOOM_limma = voomcounts, row.names = allgenes)
-       } else if ((doDESeq2==T) && (doedgeR==T))  {
-         vennmain = paste(mt,'DESeq2 and edgeR overlap at FDR=',fdrthresh)
-         counts.dataframe = data.frame(edgeR = edgeRcounts, DESeq2 = DESeqcounts, row.names = allgenes)
-       } else if ((doVoom==T) && (doedgeR==T)) {
-        vennmain = paste(mt,'Voom and edgeR overlap at FDR=',fdrthresh)
-        counts.dataframe = data.frame(edgeR = edgeRcounts, VOOM_limma = voomcounts, row.names = allgenes)
-       }
-    
-    if (nrow(counts.dataframe > 1)) {
-      counts.venn = vennCounts(counts.dataframe)
-      vennf = "Venn_significant_genes_overlap.pdf" 
-      pdf(vennf)
-      vennDiagram(counts.venn,main=vennmain,col="maroon")
-      dev.off()
-    }
-  } #### doDESeq2 or doVoom
-  
-}
-#### Done
-
-###sink(stdout(),append=T,type="message")
-builtin_gmt=""
-history_gmt=""
-out_edgeR = F
-out_DESeq2 = F
-out_VOOM = "$out_VOOM"
-doDESeq2 = $DESeq2.doDESeq2 # make these T or F
-doVoom = $doVoom
-doCamera = F 
-doedgeR = $edgeR.doedgeR
-edgeR_priordf = 0
-
-
-#if $doVoom == "T":
-  out_VOOM = "$out_VOOM"
-#end if
-
-#if $DESeq2.doDESeq2 == "T":
-  out_DESeq2 = "$out_DESeq2"
-  DESeq_fitType = "$DESeq2.DESeq_fitType"
-#end if
-
-#if $edgeR.doedgeR == "T":
-  out_edgeR = "$out_edgeR"
-  edgeR_priordf = $edgeR.edgeR_priordf
-#end if
-
-if (sum(c(doedgeR,doVoom,doDESeq2)) == 0)
-{
-write("No methods chosen - nothing to do! Please try again after choosing one or more methods", stderr())
-quit(save="no",status=2)
-}
-
-Out_Dir = "$html_file.files_path"
-Input =  "$input1"
-TreatmentName = "$treatment_name"
-TreatmentCols = "$Treat_cols"
-ControlName = "$control_name"
-ControlCols= "$Control_cols"
-org = "$input1.dbkey"
-if (org == "") { org = "hg19"}
-fdrtype = "$fdrtype"
-fdrthresh = $fdrthresh
-useNDF = $useNDF
-fQ = $fQ # non-differential centile cutoff
-myTitle = "$title"
-subjects = c($subjectids)
-nsubj = length(subjects)
-TCols = as.numeric(strsplit(TreatmentCols,",")[[1]])-1
-CCols = as.numeric(strsplit(ControlCols,",")[[1]])-1 
-cat('Got TCols=')
-cat(TCols)
-cat('; CCols=')
-cat(CCols)
-cat('\n')
-useCols = c(TCols,CCols)
-if (file.exists(Out_Dir) == F) dir.create(Out_Dir)
-Count_Matrix = read.table(Input,header=T,row.names=1,sep='\t') #Load tab file assume header
-snames = colnames(Count_Matrix)
-nsamples = length(snames)
-if (nsubj >  0 & nsubj != nsamples) {
-options("show.error.messages"=T)
-mess = paste('Fatal error: Supplied subject id list',paste(subjects,collapse=','),
-   'has length',nsubj,'but there are',nsamples,'samples',paste(snames,collapse=','))
-write(mess, stderr())
-quit(save="no",status=4)
-}
-
-Count_Matrix = Count_Matrix[,useCols] ### reorder columns
-if (length(subjects) != 0) {subjects = subjects[useCols]}
-rn = rownames(Count_Matrix)
-islib = rn %in% c('librarySize','NotInBedRegions')
-LibSizes = Count_Matrix[subset(rn,islib),][1] # take first
-Count_Matrix = Count_Matrix[subset(rn,! islib),]
-group = c(rep(TreatmentName,length(TCols)), rep(ControlName,length(CCols)) )             #Build a group descriptor
-group = factor(group, levels=c(ControlName,TreatmentName))
-colnames(Count_Matrix) = paste(group,colnames(Count_Matrix),sep="_")                   #Relable columns
-results = edgeIt(Count_Matrix=Count_Matrix,group=group, out_edgeR=out_edgeR, out_VOOM=out_VOOM, out_DESeq2=out_DESeq2,
-                 fdrtype='BH',priordf=edgeR_priordf,fdrthresh=0.05,outputdir='.',
-                 myTitle=myTitle,useNDF=F,libSize=c(),filterquantile=fQ,subjects=c(),
-                 doDESeq2=doDESeq2,doVoom=doVoom,doCamera=doCamera,doedgeR=doedgeR,org=org,
-                 histgmt=history_gmt,bigmt=builtin_gmt,DESeq_fitType=DESeq_fitType)
-sessionInfo()
-]]>
-</configfile>
-</configfiles>
-<help>
-
-----
-
-**What it does**
-
-Allows short read sequence counts from controlled experiments to be analysed for differentially expressed genes.
-Optionally adds a term for subject if not all samples are independent or if some other factor needs to be blocked in the design.
-
-**Input**
-
-Requires a count matrix as a tabular file. These are best made using the companion HTSeq_ based counter Galaxy wrapper
-and your fave gene model to generate inputs. Each row is a genomic feature (gene or exon eg) and each column the 
-non-negative integer count of reads from one sample overlapping the feature. 
-The matrix must have a header row uniquely identifying the source samples, and unique row names in 
-the first column. Typically the row names are gene symbols or probe ids for downstream use in GSEA and other methods.
-
-**Specifying comparisons**
-
-This is basically dumbed down for two factors - case vs control.
-
-More complex interfaces are possible but painful at present. 
-Probably need to specify a phenotype file to do this better.
-Work in progress. Send code.
-
-If you have (eg) paired samples and wish to include a term in the GLM to account for some other factor (subject in the case of paired samples),
-put a comma separated list of indicators for every sample (whether modelled or not!) indicating (eg) the subject number or 
-A list of integers, one for each subject or an empty string if samples are all independent.
-If not empty, there must be exactly as many integers in the supplied integer list as there are columns (samples) in the count matrix.
-Integers for samples that are not in the analysis *must* be present in the string as filler even if not used.
-
-So if you have 2 pairs out of 6 samples, you need to put in unique integers for the unpaired ones
-eg if you had 6 samples with the first two independent but the second and third pairs each being from independent subjects. you might use
-8,9,1,1,2,2 
-as subject IDs to indicate two paired samples from the same subject in columns 3/4 and 5/6
-
-**Methods available**
-
-You can run 3 popular Bioconductor packages available for count data.
-
-edgeR - see edgeR_ for details
-
-VOOM/limma - see limma_VOOM_ for details
-
-DESeq2 - see DESeq2_ for details
-
-and optionally camera in edgeR which works better if MSigDB is installed.
-
-**Outputs**
-
-Some helpful plots and analysis results. Note that most of these are produced using R code 
-suggested by the excellent documentation and vignettes for the Bioconductor
-packages invoked. The Tool Factory is used to automatically lay these out for you to enjoy.
-
-**Note on Voom**
-
-The voom from limma version 3.16.6 help in R includes this from the authors - but you should read the paper to interpret this method.
-
-This function is intended to process RNA-Seq or ChIP-Seq data prior to linear modelling in limma.
-
-voom is an acronym for mean-variance modelling at the observational level.
-The key concern is to estimate the mean-variance relationship in the data, then use this to compute appropriate weights for each observation.
-Count data almost show non-trivial mean-variance relationships. Raw counts show increasing variance with increasing count size, while log-counts typically show a decreasing mean-variance trend.
-This function estimates the mean-variance trend for log-counts, then assigns a weight to each observation based on its predicted variance.
-The weights are then used in the linear modelling process to adjust for heteroscedasticity.
-
-In an experiment, a count value is observed for each tag in each sample. A tag-wise mean-variance trend is computed using lowess.
-The tag-wise mean is the mean log2 count with an offset of 0.5, across samples for a given tag.
-The tag-wise variance is the quarter-root-variance of normalized log2 counts per million values with an offset of 0.5, across samples for a given tag.
-Tags with zero counts across all samples are not included in the lowess fit. Optional normalization is performed using normalizeBetweenArrays.
-Using fitted values of log2 counts from a linear model fit by lmFit, variances from the mean-variance trend were interpolated for each observation.
-This was carried out by approxfun. Inverse variance weights can be used to correct for mean-variance trend in the count data.
-
-
-Author(s)
-
-Charity Law and Gordon Smyth
-
-References
-
-Law, CW (2013). Precision weights for gene expression analysis. PhD Thesis. University of Melbourne, Australia.
-
-Law, CW, Chen, Y, Shi, W, Smyth, GK (2013). Voom! Precision weights unlock linear model analysis tools for RNA-seq read counts.
-Technical Report 1 May 2013, Bioinformatics Division, Walter and Eliza Hall Institute of Medical Reseach, Melbourne, Australia.
-http://www.statsci.org/smyth/pubs/VoomPreprint.pdf
-
-See Also
-
-A voom case study is given in the edgeR User's Guide.
-
-vooma is a similar function but for microarrays instead of RNA-seq.
-
-
-***old rant on changes to Bioconductor package variable names between versions***
-
-The edgeR authors made a small cosmetic change in the name of one important variable (from p.value to PValue) 
-breaking this and all other code that assumed the old name for this variable, 
-between edgeR2.4.4 and 2.4.6 (the version for R 2.14 as at the time of writing). 
-This means that all code using edgeR is sensitive to the version. I think this was a very unwise thing 
-to do because it wasted hours of my time to track down and will similarly cost other edgeR users dearly
-when their old scripts break. This tool currently now works with 2.4.6.
-
-**Note on prior.N**
-
-http://seqanswers.com/forums/showthread.php?t=5591 says:
-
-*prior.n*
-
-The value for prior.n determines the amount of smoothing of tagwise dispersions towards the common dispersion. 
-You can think of it as like a "weight" for the common value. (It is actually the weight for the common likelihood 
-in the weighted likelihood equation). The larger the value for prior.n, the more smoothing, i.e. the closer your 
-tagwise dispersion estimates will be to the common dispersion. If you use a prior.n of 1, then that gives the 
-common likelihood the weight of one observation.
-
-In answer to your question, it is a good thing to squeeze the tagwise dispersions towards a common value, 
-or else you will be using very unreliable estimates of the dispersion. I would not recommend using the value that 
-you obtained from estimateSmoothing()---this is far too small and would result in virtually no moderation 
-(squeezing) of the tagwise dispersions. How many samples do you have in your experiment? 
-What is the experimental design? If you have few samples (less than 6) then I would suggest a prior.n of at least 10. 
-If you have more samples, then the tagwise dispersion estimates will be more reliable, 
-so you could consider using a smaller prior.n, although I would hesitate to use a prior.n less than 5. 
-
-
-From Bioconductor Digest, Vol 118, Issue 5, Gordon writes:
-
-Dear Dorota,
-
-The important settings are prior.df and trend.
-
-prior.n and prior.df are related through prior.df = prior.n * residual.df,
-and your experiment has residual.df = 36 - 12 = 24.  So the old setting of
-prior.n=10 is equivalent for your data to prior.df = 240, a very large
-value.  Going the other way, the new setting of prior.df=10 is equivalent
-to prior.n=10/24.
-
-To recover old results with the current software you would use
-
-  estimateTagwiseDisp(object, prior.df=240, trend="none")
-
-To get the new default from old software you would use
-
-  estimateTagwiseDisp(object, prior.n=10/24, trend=TRUE)
-
-Actually the old trend method is equivalent to trend="loess" in the new
-software. You should use plotBCV(object) to see whether a trend is
-required.
-
-Note you could also use
-
-  prior.n = getPriorN(object, prior.df=10)
-
-to map between prior.df and prior.n.
-
-----
-
-**Attributions**
-
-edgeR - edgeR_ 
-
-VOOM/limma - limma_VOOM_ 
-
-DESeq2 - DESeq2_ for details
-
-See above for Bioconductor package documentation for packages exposed in Galaxy by this tool and app store package.
-
-Galaxy_ (that's what you are using right now!) for gluing everything together 
-
-Otherwise, all code and documentation comprising this tool was written by Ross Lazarus and is 
-licensed to you under the LGPL_ like other rgenetics artefacts
-
-.. _LGPL: http://www.gnu.org/copyleft/lesser.html
-.. _HTSeq: http://www-huber.embl.de/users/anders/HTSeq/doc/index.html
-.. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
-.. _DESeq2: http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
-.. _limma_VOOM: http://www.bioconductor.org/packages/release/bioc/html/limma.html
-.. _Galaxy: http://getgalaxy.org
-</help>
-
-</tool>
-
-

--- a/rgedgeR/test-data/edgeRtest1out.html	Sat Jul 27 22:28:00 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,813 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> 
-        <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> 
-        <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> 
-        <meta name="generator" content="Galaxy rgToolFactory.py tool output - see http://g2.trac.bx.psu.edu/" /> 
-        <title></title> 
-        <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> 
-        </head> 
-        <body> 
-        <div class="toolFormBody"> 
-        
-<div class="infomessage">Galaxy Tool "edgeR" run at 12/06/2013 16:42:51</div><br/>
-<div><table class="simple" cellpadding="2" cellspacing="2">
-<tr>
-<td><a href="edgeRtest_BCV_vs_abundance.pdf"><img src="edgeRtest_BCV_vs_abundance.jpg" title="Click to download a PDF of edgeRtest_BCV_vs_abundance.pdf" hspace="5" width="400" 
-                       alt="Image called edgeRtest_BCV_vs_abundance.pdf"/></a></td>
-
-<td><a href="edgeRtest_MDSplot.pdf"><img src="edgeRtest_MDSplot.jpg" title="Click to download a PDF of edgeRtest_MDSplot.pdf" hspace="5" width="400" 
-                       alt="Image called edgeRtest_MDSplot.pdf"/></a></td>
-
-<td><a href="edgeRtest_RowsumCum.pdf"><img src="edgeRtest_RowsumCum.jpg" title="Click to download a PDF of edgeRtest_RowsumCum.pdf" hspace="5" width="400" 
-                       alt="Image called edgeRtest_RowsumCum.pdf"/></a></td>
-</tr>
-<tr>
-<td><a href="edgeRtest_Smearplot.pdf"><img src="edgeRtest_Smearplot.jpg" title="Click to download a PDF of edgeRtest_Smearplot.pdf" hspace="5" width="400" 
-                       alt="Image called edgeRtest_Smearplot.pdf"/></a></td>
-
-<td><a href="edgeRtest_heatmap.pdf"><img src="edgeRtest_heatmap.jpg" title="Click to download a PDF of edgeRtest_heatmap.pdf" hspace="5" width="400" 
-                       alt="Image called edgeRtest_heatmap.pdf"/></a></td>
-
-<td><a href="edgeRtest_pval_qq.pdf"><img src="edgeRtest_pval_qq.jpg" title="Click to download a PDF of edgeRtest_pval_qq.pdf" hspace="5" width="400" 
-                       alt="Image called edgeRtest_pval_qq.pdf"/></a></td>
-</tr>
-<tr>
-<td><a href="edgeRtest_sampleBoxplot.pdf"><img src="edgeRtest_sampleBoxplot.jpg" title="Click to download a PDF of edgeRtest_sampleBoxplot.pdf" hspace="5" width="400" 
-                       alt="Image called edgeRtest_sampleBoxplot.pdf"/></a></td>
-
-<td><a href="edgeRtest_samplehistplot.pdf"><img src="edgeRtest_samplehistplot.jpg" title="Click to download a PDF of edgeRtest_samplehistplot.pdf" hspace="5" width="400" 
-                       alt="Image called edgeRtest_samplehistplot.pdf"/></a></td>
-
-<td><a href="edgeRtest_venn.pdf"><img src="edgeRtest_venn.jpg" title="Click to download a PDF of edgeRtest_venn.pdf" hspace="5" width="400" 
-                       alt="Image called edgeRtest_venn.pdf"/></a></td>
-</tr>
-<tr>
-<td><a href="edgeRtest_voomplot.pdf"><img src="edgeRtest_voomplot.jpg" title="Click to download a PDF of edgeRtest_voomplot.pdf" hspace="5" width="400" 
-                       alt="Image called edgeRtest_voomplot.pdf"/></a></td>
-
-<td>&nbsp;</td><td>&nbsp;</td>
-</tr></table></div>
-
-<div><table class="colored" cellpadding="3" cellspacing="3"><tr><th>Output File Name (click to view)</th><th>Size</th></tr>
-
-<tr><td><a href="edgeR.Rscript">edgeR.Rscript</a></td><td>19.7 KB)</td></tr>
-<tr class="odd_row"><td><a href="edgeR_runner.log">edgeR_runner.log</a></td><td>79.2 KB)</td></tr>
-<tr><td><a href="edgeRtest_BCV_vs_abundance.pdf">edgeRtest_BCV_vs_abundance.pdf</a></td><td>16.4 KB)</td></tr>
-<tr class="odd_row"><td><a href="edgeRtest_DESeq_TopTable.xls">edgeRtest_DESeq_TopTable.xls</a></td><td>135.1 KB)</td></tr>
-<tr><td><a href="edgeRtest_MDSplot.pdf">edgeRtest_MDSplot.pdf</a></td><td>4.9 KB)</td></tr>
-<tr class="odd_row"><td><a href="edgeRtest_RowsumCum.pdf">edgeRtest_RowsumCum.pdf</a></td><td>6.3 KB)</td></tr>
-<tr><td><a href="edgeRtest_Smearplot.pdf">edgeRtest_Smearplot.pdf</a></td><td>16.7 KB)</td></tr>
-<tr class="odd_row"><td><a href="edgeRtest_VOOM_topTable.xls">edgeRtest_VOOM_topTable.xls</a></td><td>131.4 KB)</td></tr>
-<tr><td><a href="edgeRtest_heatmap.pdf">edgeRtest_heatmap.pdf</a></td><td>11.3 KB)</td></tr>
-<tr class="odd_row"><td><a href="edgeRtest_pval_qq.pdf">edgeRtest_pval_qq.pdf</a></td><td>15.9 KB)</td></tr>
-<tr><td><a href="edgeRtest_sampleBoxplot.pdf">edgeRtest_sampleBoxplot.pdf</a></td><td>7.8 KB)</td></tr>
-<tr class="odd_row"><td><a href="edgeRtest_samplehistplot.pdf">edgeRtest_samplehistplot.pdf</a></td><td>10.9 KB)</td></tr>
-<tr><td><a href="edgeRtest_venn.pdf">edgeRtest_venn.pdf</a></td><td>9.7 KB)</td></tr>
-<tr class="odd_row"><td><a href="edgeRtest_voomplot.pdf">edgeRtest_voomplot.pdf</a></td><td>16.7 KB)</td></tr>
-</table></div><br/>
-<div class="toolFormTitle">Rscript log</div><pre>
-
-## Toolfactory generated command line = Rscript - None /data/home/rlazarus/galaxy-central/database/files/000/dataset_2.dat
-
-Loading required package: gtools
-
-Loading required package: gdata
-
-gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
-
-gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
-
-Attaching package: ‘gdata’
-
-The following object(s) are masked from ‘package:stats’:
-
-    nobs
-
-The following object(s) are masked from ‘package:utils’:
-
-    object.size
-
-Loading required package: caTools
-
-Loading required package: grid
-
-Loading required package: KernSmooth
-
-KernSmooth 2.23 loaded
-
-Copyright M. P. Wand 1997-2009
-
-Loading required package: MASS
-
-Attaching package: ‘gplots’
-
-The following object(s) are masked from ‘package:stats’:
-
-    lowess
-
-Loading required package: Biobase
-
-Loading required package: BiocGenerics
-
-Loading required package: methods
-
-Attaching package: ‘BiocGenerics’
-
-The following object(s) are masked from ‘package:gdata’:
-
-    combine
-
-The following object(s) are masked from ‘package:stats’:
-
-    xtabs
-
-The following object(s) are masked from ‘package:base’:
-
-    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
-
-    get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
-
-    pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
-
-    rownames, sapply, setdiff, table, tapply, union, unique
-
-Welcome to Bioconductor
-
-    Vignettes contain introductory material; view with
-
-    'browseVignettes()'. To cite Bioconductor, see
-
-    'citation("Biobase")', and for packages 'citation("pkgname")'.
-
-Loading required package: locfit
-
-locfit 1.5-9.1 	 2013-03-22
-
-Loading required package: lattice
-
-Warning message:
-
-found methods to import for function ‘eapply’ but not the generic itself 
-
-Loading required package: limma
-
-Attaching package: ‘limma’
-
-The following object(s) are masked from ‘package:DESeq’:
-
-    plotMA
-
-# got TCols=2 3 4 8; CCols=1 5 6 7
-
-[1] # Quantiles for non-zero row counts:
-
-       0%       10%       20%       30%       40%       50%       60%       70%       80%       90%      100% 
-
-      1.0       1.0       2.0       3.0       4.0       8.0      13.0      24.0      86.6     753.0 2325567.0 
-
-[1] Read 3242 contigs. Removed 1494 with no reads. After filtering at count quantile =0.3, there are 1141 contigs
-
-[1] # Total low count contigs per sample =  145,111,155,120,170,67,203,86
-
-Calculating library sizes from column totals.
-
-[1] Using samples: case_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam,case_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam,case_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam,case_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam,control_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam,control_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam,control_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam,control_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam
-
-[1] Using design matrix:
-
-  (Intercept) groupcase
-
-1           1         1
-
-2           1         1
-
-3           1         1
-
-4           1         1
-
-5           1         0
-
-6           1         0
-
-7           1         0
-
-8           1         0
-
-attr(,"assign")
-
-[1] 0 1
-
-attr(,"contrasts")
-
-attr(,"contrasts")$group
-
-[1] contr.treatment
-
-[1] "No GLM fit outlier genes found\n"
-
-[1] Common Dispersion = 0.24088423096811 CV =  0.490799583300669 getPriorN =  3.33333333333333
-
-[1] "Raw sample read totals 1440960,1341813,2888924,1428365,2443751,1644652,1682104,1806045"
-
-[1] raw contig counts by sample:
-
- case_X11706He_AGTTCC case_X11699He_GGCTAC case_X11698He_TAGCTT case_X11700He_CTTGTA control_X11706Liv_CA control_X11700Liv_AT control_X11698Liv_AC control_X11699Liv_AT
-
- Min.   :0.0043       Min.   :0.0043       Min.   :0.0043       Min.   :0.0043       Min.   :0.0043       Min.   :0.0043       Min.   :0.0043       Min.   :0.0043      
-
- 1st Qu.:0.0043       1st Qu.:0.0043       1st Qu.:0.0043       1st Qu.:0.0043       1st Qu.:0.3032       1st Qu.:0.0043       1st Qu.:0.3032       1st Qu.:0.0043      
-
- Median :0.4786       Median :0.4786       Median :0.4786       Median :0.4786       Median :0.7789       Median :0.6031       Median :0.6998       Median :0.6031      
-
- Mean   :0.9210       Mean   :0.9428       Mean   :1.0205       Mean   :0.9753       Mean   :1.0519       Mean   :1.0343       Mean   :0.9855       Mean   :0.9966      
-
- 3rd Qu.:1.5770       3rd Qu.:1.5855       3rd Qu.:1.7161       3rd Qu.:1.6022       3rd Qu.:1.5410       3rd Qu.:1.6335       3rd Qu.:1.4473       3rd Qu.:1.5534      
-
- Max.   :5.3609       Max.   :5.3589       Max.   :5.6967       Max.   :5.3702       Max.   :5.8209       Max.   :5.6905       Max.   :5.7999       Max.   :5.7215      
-
- NA's   :902          NA's   :957          NA's   :821          NA's   :950          NA's   :650          NA's   :969          NA's   :664          NA's   :886         
-
-[1] normalised contig counts by sample:
-
- case_X11706He_AGTTCC case_X11699He_GGCTAC case_X11698He_TAGCTT case_X11700He_CTTGTA control_X11706Liv_CA control_X11700Liv_AT control_X11698Liv_AC control_X11699Liv_AT
-
- Min.   :-Inf         Min.   :-Inf         Min.   :-Inf         Min.   :-Inf         Min.   :-Inf         Min.   :-Inf         Min.   :-Inf         Min.   :-Inf        
-
- 1st Qu.:-Inf         1st Qu.:-Inf         1st Qu.:-Inf         1st Qu.:-Inf         1st Qu.:   0         1st Qu.:-Inf         1st Qu.:   0         1st Qu.:-Inf        
-
- Median :   0         Median :   0         Median :   0         Median :   0         Median :   0         Median :   0         Median :   0         Median :   0        
-
- Mean   :-Inf         Mean   :-Inf         Mean   :-Inf         Mean   :-Inf         Mean   :-Inf         Mean   :-Inf         Mean   :-Inf         Mean   :-Inf        
-
- 3rd Qu.:   1         3rd Qu.:   1         3rd Qu.:   1         3rd Qu.:   1         3rd Qu.:   1         3rd Qu.:   1         3rd Qu.:   1         3rd Qu.:   1        
-
- Max.   :   5         Max.   :   5         Max.   :   6         Max.   :   5         Max.   :   6         Max.   :   6         Max.   :   6         Max.   :   5        
-
-[1] Using ncol rawrs= 8
-
-[1] # writing output
-
-[1] # urls
-
-<a href='http://www.genecards.org/index.php?path=/Search/keyword/0610005C13Rik'></a>0610005C13Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610007N19Rik'></a>0610007N19Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610008F07Rik'></a>0610008F07Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610009L18Rik'></a>0610009L18Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610012G03Rik'></a>0610012G03Rik</a> <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610031O16Rik'></a>0610031O16Rik</a># Top tags
-
-                       Name      logFC    logCPM        LR       PValue  adj.p.value Dispersion totreads case_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam case_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam case_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam case_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam control_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam control_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam
-
-Mir122a             Mir122a -10.661348 12.537949 445.91203 5.594743e-99 6.383602e-96 0.10205510    90428                                                   6.644669                                               2.864648e+00                                               2.012369e+01                                               4.756523e+00                                                   2.084166e+04                                                   1.681895e+04
-
-Mir192               Mir192  -7.109019 17.247415 366.13166 1.301558e-81 7.425390e-79 0.07765487  2325567                                                1779.663879                                               1.294412e+03                                               4.493546e+03                                               1.933526e+03                                                   4.635990e+05                                                   3.403123e+05
-
-Mir208b             Mir208b  13.423720  9.822338 355.41782 2.801296e-79 1.065426e-76 0.12444059    14756                                                1245.907022                                               5.701390e+02                                               4.930344e+03                                               8.819024e+02                                                   7.453220e-01                                                   0.000000e+00
-
-Mir208a             Mir208a  11.977586  8.388290 348.81540 7.675451e-78 2.189422e-75 0.09936798     4638                                                 433.789590                                               7.125278e+02                                               1.006599e+03                                               6.497485e+02                                                   0.000000e+00                                                   0.000000e+00
-
-Mir499               Mir499  14.488216  8.612770 291.12794 2.823507e-65 6.443244e-63 0.13481620     6527                                                 608.439028                                               5.066577e+02                                               2.521609e+03                                               2.703574e+02                                                   0.000000e+00                                                   0.000000e+00
-
-Mir149               Mir149   6.869731  8.785665 253.01986 5.702930e-57 1.084507e-54 0.09834684     6164                                                 774.657675                                               4.595714e+02                                               1.710514e+03                                               7.663947e+02                                                   1.750400e+01                                                   6.246465e+00
-
-Mir490               Mir490   8.453930  6.909596 251.05610 1.528281e-56 2.491098e-54 0.09745005     1741                                                 209.881557                                               2.177498e+02                                               5.205387e+02                                               1.957941e+02                                                   1.038505e+00                                                   5.537224e-01
-
-Mir802               Mir802 -12.499678  6.629391 237.56161 1.337812e-53 1.908055e-51 0.10939981     1514                                                   0.000000                                               0.000000e+00                                               0.000000e+00                                               0.000000e+00                                                   3.056548e+02                                                   1.641034e+02
-
-Mir204               Mir204   7.371179  7.558996 237.12302 1.667365e-53 2.113848e-51 0.10292005     2601                                                 425.578854                                               3.264164e+02                                               6.462477e+02                                               3.754819e+02                                                   3.040281e+00                                                   6.923364e-01
-
-Mir1948             Mir1948  -7.583326  7.293456 204.79641 1.875897e-46 2.140399e-44 0.11833999     2404                                                   1.216112                                               6.923364e-01                                               1.661167e+00                                               1.636942e+00                                                   6.476848e+02                                                   3.852783e+02
-
-Mir3073             Mir3073 -11.748556  5.881462 200.03350 2.053625e-45 2.130170e-43 0.11068562      904                                                   0.000000                                               0.000000e+00                                               0.000000e+00                                               0.000000e+00                                                   2.073471e+02                                                   7.546467e+01
-
-Mir194-2           Mir194-2  -5.439827  7.860048 165.57239 6.859199e-38 6.521955e-36 0.10671020     3570                                                  10.520726                                               6.138532e+00                                               1.490644e+01                                               9.513045e+00                                                   9.214105e+02                                                   6.003547e+02
-
-Mir10b               Mir10b   5.032898 13.880770 160.06580 1.094640e-36 9.607570e-35 0.10795434   197340                                               25838.822630                                               3.216361e+04                                               3.631730e+04                                               3.446522e+04                                                   1.825385e+03                                                   3.738617e+02
-
-Mir101b             Mir101b  -3.925287 11.936090 120.62427 4.618143e-28 3.763787e-26 0.09663075    59019                                                 219.816815                                               3.012250e+02                                               8.119232e+02                                               4.270695e+02                                                   1.014507e+04                                                   7.747970e+03
-
-Mir182               Mir182  -5.244384  8.942708 118.92815 1.085926e-27 8.260276e-26 0.14993443     7189                                                  16.962242                                               1.439678e+01                                               2.209871e+01                                               3.130352e+01                                                   9.840056e+02                                                   6.154406e+02
-
-Mir200b             Mir200b  -6.725348  5.765187 115.73189 5.440989e-27 3.880105e-25 0.16712490      888                                                   2.432225                                               0.000000e+00                                               1.661167e+00                                               0.000000e+00                                                   3.696797e+02                                                   9.750871e+01
-
-Mir181c             Mir181c   3.611867 10.569815 107.82011 2.943153e-25 1.975375e-23 0.09385270    23605                                                2420.852087                                               1.892879e+03                                               4.093093e+03                                               1.902590e+03                                                   2.320365e+02                                                   2.727878e+02
-
-Mir181d             Mir181d   3.489976  7.232064 102.18661 5.053019e-24 3.203053e-22 0.08738498     2139                                                 310.053946                                               2.021522e+02                                               5.398233e+02                                               2.956660e+02                                                   3.648337e+01                                                   1.453906e+01
-
-Mir21                 Mir21  -3.077771 13.881500  91.37324 1.189745e-21 7.144733e-20 0.08494272   229120                                                3207.212585                                               2.190826e+03                                               4.348911e+03                                               2.010566e+03                                                   2.715400e+04                                                   3.322794e+04
-
-Mir199b             Mir199b   5.411476  4.695869  86.70372 1.260596e-20 7.191701e-19 0.15656183      370                                                  43.403268                                               4.481024e+01                                               9.924938e+01                                               4.925255e+01                                                   1.384673e+00                                                   5.537224e-01
-
-Mir193               Mir193  -5.360157  4.775477  84.66127 3.541205e-20 1.924055e-18 0.15546497      421                                                   1.490644                                               1.189131e+00                                               2.800640e+00                                               6.940516e-01                                                   1.015454e+02                                                   3.496299e+01
-
-Mir23a               Mir23a   3.003071  9.467420  82.28684 1.177029e-19 6.104501e-18 0.08920345    10118                                                1149.889322                                               1.127958e+03                                               2.471518e+03                                               1.096325e+03                                                   1.505832e+02                                                   1.268024e+02
-
-Mir195               Mir195   3.060546  8.152797  81.39727 1.846126e-19 9.158392e-18 0.09133016     3962                                                 429.134881                                               2.831909e+02                                               9.227086e+02                                               4.708957e+02                                                   1.106253e+02                                                   7.773378e+01
-
-Ahsg                   Ahsg -10.101343  6.638589  79.82133 4.098447e-19 1.923759e-17 0.42092199     1524                                                   0.000000                                               5.537224e-01                                               0.000000e+00                                               0.000000e+00                                                   3.484153e+02                                                   1.260288e+01
-
-Mir148a             Mir148a  -2.789375 16.047169  79.76589 4.215073e-19 1.923759e-17 0.08196054  1002397                                               15925.598251                                               8.528200e+03                                               2.207082e+04                                               1.059020e+04                                                   1.927239e+05                                                   1.054456e+05
-
-Dnm3os               Dnm3os   3.189443  6.618834  79.19614 5.623979e-19 2.468062e-17 0.09496531     1401                                                 134.000827                                               8.716715e+01                                               3.652078e+02                                               1.825316e+02                                                   3.710848e+01                                                   2.498586e+01
-
-Mir27a               Mir27a   2.921772 10.581277  77.26988 1.491231e-18 6.301832e-17 0.09125059    21886                                                2383.612353                                               2.512174e+03                                               5.321988e+03                                               2.361690e+03                                                   3.285136e+02                                                   3.477377e+02
-
-Mir429               Mir429  -5.341934  4.951103  76.38758 2.331128e-18 9.499346e-17 0.18324117      499                                                   1.783696                                               7.001600e-01                                               2.082155e+00                                               1.824168e+00                                                   9.173458e+01                                                   4.540524e+01
-
-Mir214               Mir214   3.125906  6.202347  74.28213 6.771387e-18 2.664191e-16 0.09532762     1048                                                 110.058161                                               5.642542e+01                                               1.982326e+02                                               9.371492e+01                                                   3.353949e+01                                                   1.545870e+01
-
-Mir200a             Mir200a  -7.592263  4.059943  73.71426 9.028450e-18 3.433821e-16 0.22417820      264                                                   0.000000                                               0.000000e+00                                               5.945653e-01                                               0.000000e+00                                                   9.022671e+01                                                   3.222698e+01
-
-Mir194-1           Mir194-1  -3.970219  5.393899  73.22380 1.157517e-17 4.260408e-16 0.13095886      635                                                   3.567392                                               9.102080e+00                                               5.552413e+00                                               3.648337e+00                                                   7.615701e+01                                                   8.859559e+01
-
-Mir378               Mir378   2.954320  8.053368  73.09647 1.234655e-17 4.402315e-16 0.09566655     4075                                                 425.697272                                               3.921392e+02                                               1.155915e+03                                               1.883155e+02                                                   7.641369e+01                                                   3.683119e+01
-
-Mir322               Mir322   3.058569  8.948242  72.83721 1.407969e-17 4.868160e-16 0.10365695     7074                                                1012.892580                                               6.718588e+02                                               1.784708e+03                                               8.550716e+02                                                   1.587027e+02                                                   7.892635e+01
-
-Mir215               Mir215   2.908934  6.381924  70.31105 5.065317e-17 1.699861e-15 0.09002036     1182                                                 123.075020                                               1.610368e+02                                               2.727623e+02                                               1.222193e+02                                                   1.938542e+01                                                   1.716540e+01
-
-Cyp3a25             Cyp3a25  -9.778602  3.913257  70.02642 5.851533e-17 1.907600e-15 0.26445237      226                                                   0.000000                                               0.000000e+00                                               0.000000e+00                                               0.000000e+00                                                   5.664447e+01                                                   1.783696e+01
-
-Mir183               Mir183  -4.214462  5.247929  66.31101 3.851010e-16 1.220556e-14 0.15955164      563                                                   8.401920                                               1.388103e+00                                               2.432225e+00                                               2.423177e+00                                                   8.638070e+01                                                   2.905572e+01
-
-Mir181a-2         Mir181a-2   2.837713  7.573798  65.52900 5.726500e-16 1.765929e-14 0.09834030     2817                                                 288.826664                                               1.377749e+02                                               6.395494e+02                                               1.821098e+02                                                   5.813511e+01                                                   4.102501e+01
-
-Mir155               Mir155   3.734310  4.975364  65.07600 7.206449e-16 2.163831e-14 0.13295455      463                                                  33.966543                                               5.888044e+01                                               1.141565e+02                                               5.251200e+01                                                   9.716723e+00                                                   1.824168e+00
-
-Snord91a           Snord91a  -2.818342  6.592251  64.29345 1.072014e-15 3.136329e-14 0.09422446     1437                                                  13.846728                                               1.605795e+01                                               3.314807e+01                                               1.863305e+01                                                   2.158272e+02                                                   1.792410e+02
-
-Mir125b-2         Mir125b-2   2.852233  8.081093  64.20822 1.119409e-15 3.193115e-14 0.10276578     3837                                                 315.520541                                               4.404853e+02                                               7.634219e+02                                               4.852109e+02                                                   1.082721e+02                                                   9.060036e+01
-
-Serpina4-ps1   Serpina4-ps1 -10.090564  4.224051  64.02094 1.231040e-15 3.425894e-14 0.34406452      295                                                   0.000000                                               0.000000e+00                                               0.000000e+00                                               0.000000e+00                                                   1.080717e+02                                                   1.129674e+01
-
-Mir133b             Mir133b   9.293392  3.404704  63.59576 1.527577e-15 4.149919e-14 0.26404392      159                                                  17.719118                                               1.064012e+01                                               5.738979e+01                                               1.426957e+01                                                   0.000000e+00                                                   0.000000e+00
-
-Gm10069             Gm10069  -7.475459  6.400326  63.15445 1.911172e-15 5.071271e-14 0.41541432     1309                                                   1.189131                                               1.400320e+00                                               6.940516e-01                                               6.080561e-01                                                   1.914310e+02                                                   6.644669e+00
-
-Mir871               Mir871  -5.633588  4.283233  62.67513 2.437746e-15 6.321517e-14 0.21907826      290                                                   1.227706                                               7.453220e-01                                               5.945653e-01                                               0.000000e+00                                                   5.691223e+01                                                   4.925255e+01
-
-Mir184               Mir184   5.002968  4.123691  61.97642 3.475940e-15 8.813439e-14 0.19289992      247                                                  33.443087                                               1.419290e+01                                               4.983502e+01                                               2.168948e+01                                                   2.981288e+00                                                   0.000000e+00
-
-Mir132               Mir132   2.702863  5.866134  58.80773 1.738573e-14 4.312416e-13 0.09148478      857                                                  82.695634                                               4.327103e+01                                               1.821747e+02                                               6.097608e+01                                                   2.832224e+01                                                   1.308044e+01
-
-Snord104           Snord104  -2.492063 11.108871  58.55547 1.976394e-14 4.798012e-13 0.09093023    33458                                                 614.929745                                               4.378004e+02                                               8.629974e+02                                               5.144081e+02                                                   3.826761e+03                                                   4.181256e+03
-
-Mir3074-2         Mir3074-2   2.635505  7.871042  57.72938 3.007773e-14 7.149726e-13 0.09900198     3470                                                 450.903031                                               3.206519e+02                                               8.354691e+02                                               1.716994e+02                                                   8.970303e+01                                                   5.197290e+01
-
-Mir24-2             Mir24-2   2.635505  7.871042  57.68174 3.081509e-14 7.175515e-13 0.09908656     3470                                                 479.987359                                               2.746892e+02                                               9.620198e+02                                               3.442496e+02                                                   9.850509e+01                                                   4.396336e+01
-
-5430416N02Rik 5430416N02Rik  -3.267228  5.202367  56.75137 4.945455e-14 1.128553e-12 0.12456687      564                                                   6.080561                                               1.730841e+00                                               1.273562e+01                                               4.910826e+00                                                   1.453378e+02                                                   5.886197e+01
-
-              control_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam control_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam case_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam case_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam case_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam case_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam control_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam
-
-Mir122a                                                         7.242557e+03                                                   8.468313e+03                                                         12                                                          7                                                         27                                                          8                                                          29767
-
-Mir192                                                          3.835916e+05                                                   1.822922e+05                                                       3214                                                       3163                                                       6029                                                       3252                                                         662133
-
-Mir208b                                                         0.000000e+00                                                   0.000000e+00                                                       2049                                                       1647                                                       8904                                                       2155                                                              1
-
-Mir208a                                                         0.000000e+00                                                   5.537224e-01                                                       1060                                                        956                                                       1693                                                        928                                                              0
-
-Mir499                                                          0.000000e+00                                                   0.000000e+00                                                        869                                                        730                                                       4147                                                        781                                                              0
-
-Mir149                                                          4.864449e+00                                                   5.538691e+00                                                       1399                                                       1123                                                       2295                                                       1289                                                             25
-
-Mir490                                                          0.000000e+00                                                   7.453220e-01                                                        353                                                        311                                                        750                                                        322                                                              3
-
-Mir802                                                          1.557723e+02                                                   2.092870e+02                                                          0                                                          0                                                          0                                                          0                                                            552
-
-Mir204                                                          5.537224e-01                                                   3.683119e+00                                                        571                                                        549                                                        923                                                        541                                                              5
-
-Mir1948                                                         1.813414e+02                                                   4.282299e+02                                                          2                                                          2                                                          3                                                          4                                                            869
-
-Mir3073                                                         7.253764e+01                                                   8.757639e+01                                                          0                                                          0                                                          0                                                          0                                                            341
-
-Mir194-2                                                        2.669366e+02                                                   3.046280e+02                                                         19                                                         15                                                         20                                                         16                                                           1316
-
-Mir10b                                                          6.583760e+02                                                   7.272114e+02                                                      34668                                                      54096                                                      51870                                                      49658                                                           3002
-
-Mir101b                                                         1.128042e+04                                                   6.628420e+03                                                        635                                                        544                                                       1984                                                        573                                                          17063
-
-Mir182                                                          2.366022e+03                                                   6.536603e+02                                                         49                                                         26                                                         54                                                         42                                                           1655
-
-Mir200b                                                         4.621056e+01                                                   1.075780e+02                                                          4                                                          0                                                          3                                                          0                                                            496
-
-Mir181c                                                         2.283131e+02                                                   2.989683e+02                                                       3488                                                       3113                                                      11824                                                       3436                                                            567
-
-Mir181d                                                         2.547123e+01                                                   1.555095e+01                                                        416                                                        340                                                        771                                                        426                                                             60
-
-Mir21                                                           2.570722e+04                                                   3.537908e+04                                                       4621                                                       3603                                                      12563                                                       3631                                                          66353
-
-Mir199b                                                         0.000000e+00                                                   2.981288e+00                                                         73                                                         64                                                        143                                                         81                                                              4
-
-Mir193                                                          3.377707e+01                                                   3.396654e+01                                                          2                                                          2                                                          4                                                          1                                                            167
-
-Mir23a                                                          8.921333e+01                                                   2.437203e+02                                                       1934                                                       1611                                                       3561                                                       1803                                                            435
-
-Mir195                                                          4.560421e+01                                                   4.154019e+01                                                        775                                                        692                                                       1238                                                        792                                                            158
-
-Ahsg                                                            6.100714e+02                                                   2.432225e+01                                                          0                                                          1                                                          0                                                          0                                                            586
-
-Mir148a                                                         1.795497e+05                                                   1.342747e+05                                                      26191                                                      24636                                                      39859                                                      25878                                                         258578
-
-Dnm3os                                                          1.216112e+01                                                   1.384673e+01                                                        242                                                        213                                                        490                                                        307                                                             53
-
-Mir27a                                                          1.636942e+02                                                   5.664447e+02                                                       4009                                                       3588                                                       7668                                                       3884                                                            949
-
-Mir429                                                          1.677865e+01                                                   7.527752e+01                                                          3                                                          1                                                          3                                                          3                                                            265
-
-Mir214                                                          1.190272e+01                                                   2.012750e+01                                                        181                                                        163                                                        358                                                        229                                                             45
-
-Mir200a                                                         1.142355e+01                                                   2.602495e+01                                                          0                                                          0                                                          1                                                          0                                                            130
-
-Mir194-1                                                        3.314807e+01                                                   1.050904e+02                                                          6                                                         13                                                          8                                                          6                                                            220
-
-Mir378                                                          9.167460e+01                                                   6.302392e+01                                                        608                                                        565                                                       1901                                                        544                                                            138
-
-Mir322                                                          5.038874e+01                                                   9.166874e+01                                                       1359                                                       1130                                                       2549                                                       1232                                                            261
-
-Mir215                                                          1.145859e+01                                                   2.683159e+01                                                        207                                                        230                                                        393                                                        201                                                             56
-
-Cyp3a25                                                         6.511488e+01                                                   1.873939e+01                                                          0                                                          0                                                          0                                                          0                                                             76
-
-Mir183                                                          1.349033e+02                                                   7.729349e+01                                                         12                                                          2                                                          4                                                          7                                                            156
-
-Mir181a-2                                                       8.051840e+01                                                   5.691223e+01                                                        475                                                        398                                                       1155                                                        445                                                             78
-
-Mir155                                                          2.769346e+00                                                   4.983502e+00                                                         83                                                         79                                                        192                                                         75                                                             14
-
-Snord91a                                                        2.484705e+02                                                   1.732960e+02                                                         40                                                         29                                                         81                                                         25                                                            363
-
-Mir125b-2                                                       2.077009e+01                                                   7.364508e+01                                                        771                                                        591                                                       1284                                                        693                                                            156
-
-Serpina4-ps1                                                    8.191872e+01                                                   9.716723e+00                                                          0                                                          0                                                          0                                                          0                                                            145
-
-Mir133b                                                         0.000000e+00                                                   0.000000e+00                                                         32                                                         26                                                         77                                                         24                                                              0
-
-Gm10069                                                         2.868741e+02                                                   2.757691e+01                                                          2                                                          2                                                          1                                                          1                                                            553
-
-Mir871                                                          1.003888e+01                                                   5.149619e+01                                                          3                                                          1                                                          1                                                          0                                                             82
-
-Mir184                                                          1.400320e+00                                                   1.388103e+00                                                         55                                                         41                                                         90                                                         53                                                              4
-
-Mir132                                                          2.100480e+01                                                   1.943345e+01                                                        136                                                        125                                                        329                                                        149                                                             38
-
-Snord104                                                        4.430701e+03                                                   4.212863e+03                                                        886                                                        720                                                       2493                                                        929                                                           9351
-
-Mir3074-2                                                       4.844593e+01                                                   8.323914e+01                                                        644                                                        462                                                       1374                                                        496                                                            162
-
-Mir24-2                                                         3.599196e+01                                                   5.729296e+01                                                        644                                                        462                                                       1374                                                        496                                                            162
-
-5430416N02Rik                                                   5.531264e+01                                                   9.786128e+01                                                         10                                                          5                                                         23                                                         12                                                            195
-
-              control_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam control_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam control_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam ntotreads                                                                                                   URL
-
-Mir122a                                                                24233                                                          11911                                                          24463     90428             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'></a>Mir122a</a>
-
-Mir192                                                                490327                                                         630849                                                         526600   2325567               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'></a>Mir192</a>
-
-Mir208b                                                                    0                                                              0                                                              0     14756             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'></a>Mir208b</a>
-
-Mir208a                                                                    0                                                              0                                                              1      4638             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'></a>Mir208a</a>
-
-Mir499                                                                     0                                                              0                                                              0      6527               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'></a>Mir499</a>
-
-Mir149                                                                     9                                                              8                                                             16      6164               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'></a>Mir149</a>
-
-Mir490                                                                     1                                                              0                                                              1      1741               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'></a>Mir490</a>
-
-Mir802                                                                   401                                                            209                                                            352      1514               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'></a>Mir802</a>
-
-Mir204                                                                     2                                                              1                                                              9      2601               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'></a>Mir204</a>
-
-Mir1948                                                                  648                                                            259                                                            617      2404             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'></a>Mir1948</a>
-
-Mir3073                                                                  218                                                            131                                                            214       904             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'></a>Mir3073</a>
-
-Mir194-2                                                                 865                                                            439                                                            880      3570           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'></a>Mir194-2</a>
-
-Mir10b                                                                  1080                                                           1189                                                           1777    197340               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'></a>Mir10b</a>
-
-Mir101b                                                                11066                                                          16253                                                          10901     59019             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'></a>Mir101b</a>
-
-Mir182                                                                   879                                                           3409                                                           1075      7189               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'></a>Mir182</a>
-
-Mir200b                                                                  164                                                             66                                                            155       888             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200b'></a>Mir200b</a>
-
-Mir181c                                                                  366                                                            384                                                            427     23605             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'></a>Mir181c</a>
-
-Mir181d                                                                   42                                                             46                                                             38      2139             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'></a>Mir181d</a>
-
-Mir21                                                                  44582                                                          43237                                                          50530    229120                 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'></a>Mir21</a>
-
-Mir199b                                                                    1                                                              0                                                              4       370             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'></a>Mir199b</a>
-
-Mir193                                                                   101                                                             61                                                             83       421               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193'></a>Mir193</a>
-
-Mir23a                                                                   229                                                            218                                                            327     10118               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'></a>Mir23a</a>
-
-Mir195                                                                   112                                                             75                                                            120      3962               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'></a>Mir195</a>
-
-Ahsg                                                                      18                                                            879                                                             40      1524                   <a href='http://www.genecards.org/index.php?path=/Search/keyword/Ahsg'></a>Ahsg</a>
-
-Mir148a                                                               177349                                                         256441                                                         193465   1002397             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'></a>Mir148a</a>
-
-Dnm3os                                                                    36                                                             20                                                             40      1401               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'></a>Dnm3os</a>
-
-Mir27a                                                                   628                                                            400                                                            760     21886               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'></a>Mir27a</a>
-
-Mir429                                                                    82                                                             41                                                            101       499               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir429'></a>Mir429</a>
-
-Mir214                                                                    26                                                             17                                                             29      1048               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'></a>Mir214</a>
-
-Mir200a                                                                   53                                                             33                                                             47       264             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200a'></a>Mir200a</a>
-
-Mir194-1                                                                 160                                                             81                                                            141       635           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-1'></a>Mir194-1</a>
-
-Mir378                                                                    90                                                            123                                                            106      4075               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'></a>Mir378</a>
-
-Mir322                                                                   228                                                             91                                                            224      7074               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'></a>Mir322</a>
-
-Mir215                                                                    31                                                             28                                                             36      1182               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'></a>Mir215</a>
-
-Cyp3a25                                                                   30                                                             93                                                             27       226             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp3a25'></a>Cyp3a25</a>
-
-Mir183                                                                    71                                                            181                                                            130       563               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir183'></a>Mir183</a>
-
-Mir181a-2                                                                 69                                                            115                                                             82      2817         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-2'></a>Mir181a-2</a>
-
-Mir155                                                                     3                                                              8                                                              9       463               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'></a>Mir155</a>
-
-Snord91a                                                                 256                                                            358                                                            285      1437           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord91a'></a>Snord91a</a>
-
-Mir125b-2                                                                149                                                             60                                                            133      3837         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'></a>Mir125b-2</a>
-
-Serpina4-ps1                                                              19                                                            117                                                             14       295   <a href='http://www.genecards.org/index.php?path=/Search/keyword/Serpina4-ps1'></a>Serpina4-ps1</a>
-
-Mir133b                                                                    0                                                              0                                                              0       159             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133b'></a>Mir133b</a>
-
-Gm10069                                                                   12                                                            701                                                             37      1309             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm10069'></a>Gm10069</a>
-
-Mir871                                                                    81                                                             29                                                             93       290               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir871'></a>Mir871</a>
-
-Mir184                                                                     0                                                              2                                                              2       247               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'></a>Mir184</a>
-
-Mir132                                                                    22                                                             30                                                             28       857               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'></a>Mir132</a>
-
-Snord104                                                                5610                                                           7452                                                           6017     33458           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'></a>Snord104</a>
-
-Mir3074-2                                                                127                                                             65                                                            140      3470         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'></a>Mir3074-2</a>
-
-Mir24-2                                                                  127                                                             65                                                            140      3470             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'></a>Mir24-2</a>
-
-5430416N02Rik                                                             99                                                             79                                                            141       564 <a href='http://www.genecards.org/index.php?path=/Search/keyword/5430416N02Rik'></a>5430416N02Rik</a>
-
-[1] # 445 tags significant at adj p= 0.05
-
-[1] # deTags
-
-[1] "0610005C13Rik" "0610007N19Rik" "0610008F07Rik" "0610012G03Rik" "0610031O16Rik" "1110038B12Rik"
-
-# DESeq top 50
-
-               id     baseMean    baseMeanA    baseMeanB   foldChange log2FoldChange         pval         padj
-
-536       Mir122a  10112.31117 2.021162e+04 1.300527e+01 6.434550e-04     -10.601873 5.488369e-57 6.262229e-54
-
-645       Mir208a    616.76981 2.430915e-01 1.233297e+03 5.073385e+03      12.308733 6.046036e-53 3.449263e-50
-
-600        Mir192 271352.97636 5.385927e+05 4.113233e+03 7.637001e-03      -7.032778 1.311798e-38 4.989204e-36
-
-568        Mir149    810.35429 1.224267e+01 1.608466e+03 1.313819e+02       7.037623 7.073079e-37 2.017596e-34
-
-791        Mir490    220.99790 9.450198e-01 4.410508e+02 4.667107e+02       8.866385 1.354865e-36 3.091803e-34
-
-642        Mir204    347.57397 3.737736e+00 6.914102e+02 1.849810e+02       7.531234 8.058436e-36 1.532446e-33
-
-844        Mir802    166.83414 3.336683e+02 0.000000e+00 0.000000e+00           -Inf 3.255469e-35 5.306414e-33
-
-698       Mir3073     98.93199 1.978640e+02 0.000000e+00 0.000000e+00           -Inf 1.111351e-28 1.585065e-26
-
-646       Mir208b   1649.77924 1.445675e-01 3.299414e+03 2.282265e+04      14.478178 7.505934e-28 9.515857e-26
-
-614       Mir1948    263.89527 5.246983e+02 3.092210e+00 5.893310e-03      -7.406706 1.534188e-26 1.750509e-24
-
-608      Mir194-2    391.65678 7.637703e+02 1.954329e+01 2.558791e-02      -5.288394 1.622682e-24 1.683163e-22
-
-796        Mir499    712.45950 0.000000e+00 1.424919e+03          Inf            Inf 2.577318e-19 2.450600e-17
-
-585       Mir181c   2765.96510 3.955399e+02 5.136390e+03 1.298577e+01       3.698860 1.942959e-17 1.705320e-15
-
-631       Mir199b     47.84725 1.818862e+00 9.387565e+01 5.161231e+01       5.689643 4.012622e-15 3.270287e-13
-
-530        Mir10b  27820.40551 1.501200e+03 5.413961e+04 3.606421e+01       5.172496 3.069912e-14 2.335180e-12
-
-586       Mir181d    275.22797 4.254569e+01 5.079103e+02 1.193800e+01       3.577489 5.204519e-14 3.711473e-12
-
-602        Mir193     45.70861 8.913819e+01 2.279021e+00 2.556728e-02      -5.289558 1.657854e-13 1.112713e-11
-
-637       Mir200a     27.09009 5.402561e+01 1.545578e-01 2.860824e-03      -8.449354 2.466964e-13 1.563781e-11
-
-722        Mir322    899.53469 1.797868e+02 1.619283e+03 9.006682e+00       3.170996 1.359804e-12 8.165978e-11
-
-756        Mir378    483.21548 1.056050e+02 8.608260e+02 8.151374e+00       3.027043 2.046396e-12 1.160965e-10
-
-523       Mir101b   6846.19683 1.280838e+04 8.840090e+02 6.901800e-02      -3.856884 2.136745e-12 1.160965e-10
-
-552       Mir133b     19.46050 0.000000e+00 3.892101e+01          Inf            Inf 2.388227e-12 1.238621e-10
-
-663        Mir23a   1289.18043 2.671574e+02 2.311203e+03 8.651093e+00       3.112882 3.093049e-12 1.534421e-10
-
-671        Mir27a   2788.72629 6.066392e+02 4.970813e+03 8.194019e+00       3.034571 5.970859e-12 2.838646e-10
-
-616        Mir195    519.86200 1.038507e+02 9.358733e+02 9.011721e+00       3.171803 6.245320e-12 2.850364e-10
-
-607      Mir194-1     71.10636 1.325374e+02 9.675354e+00 7.300095e-02      -3.775941 1.405195e-11 6.166645e-10
-
-344        Dnm3os    179.61643 3.285433e+01 3.263785e+02 9.934110e+00       3.312391 1.503324e-11 6.352936e-10
-
-590        Mir184     32.23796 1.645700e+00 6.283021e+01 3.817841e+01       5.254685 1.644760e-11 6.702396e-10
-
-582     Mir181a-2    347.82506 8.313904e+01 6.125111e+02 7.367310e+00       2.881138 2.735424e-11 1.076248e-09
-
-541     Mir125b-2    493.08516 1.122867e+02 8.738836e+02 7.782608e+00       2.960254 5.662328e-11 2.153572e-09
-
-573        Mir155     57.66182 7.341434e+00 1.079822e+02 1.470860e+01       3.878588 6.173765e-11 2.272344e-09
-
-464        Gm5441     20.24317 2.430915e-01 4.024325e+01 1.655478e+02       7.371104 6.503611e-11 2.318944e-09
-
-571        Mir153     19.90411 2.430915e-01 3.956513e+01 1.627582e+02       7.346586 8.675688e-11 2.999685e-09
-
-649         Mir21  26121.31011 4.639963e+04 5.842995e+03 1.259276e-01      -2.989333 1.048681e-10 3.519252e-09
-
-654        Mir214    134.69038 2.546966e+01 2.439111e+02 9.576536e+00       3.259504 1.338023e-10 4.361954e-09
-
-638       Mir200b     87.13638 1.725548e+02 1.717931e+00 9.955853e-03      -6.650239 2.397950e-10 7.600169e-09
-
-666       Mir24-2    424.48288 1.104079e+02 7.385578e+02 6.689355e+00       2.741867 4.542021e-10 1.363802e-08
-
-700     Mir3074-2    424.48288 1.104079e+02 7.385578e+02 6.689355e+00       2.741867 4.542021e-10 1.363802e-08
-
-845        Mir871     33.03360 6.461640e+01 1.450790e+00 2.245235e-02      -5.476990 5.839129e-10 1.708320e-08
-
-767        Mir429     49.75018 9.677270e+01 2.727653e+00 2.818618e-02      -5.148868 6.903556e-10 1.969239e-08
-
-655        Mir215    152.78082 3.329953e+01 2.722621e+02 8.176156e+00       3.031423 8.994273e-10 2.503040e-08
-
-566       Mir148a 118994.46955 2.065090e+05 3.147993e+04 1.524386e-01      -2.713700 1.022762e-09 2.772155e-08
-
-569        Mir150    553.20599 1.318948e+02 9.745171e+02 7.388592e+00       2.885299 1.044721e-09 2.772155e-08
-
-628       Mir1983     14.04997 0.000000e+00 2.809994e+01          Inf            Inf 2.859722e-09 7.415778e-08
-
-581     Mir181a-1     59.53826 1.179305e+01 1.072835e+02 9.097179e+00       3.185419 3.537731e-09 8.970115e-08
-
-784        Mir470     18.37716 3.608521e+01 6.691037e-01 1.854232e-02      -5.753034 7.467127e-09 1.852172e-07
-
-630     Mir199a-2     44.84878 7.384673e+00 8.231288e+01 1.114645e+01       3.478512 8.433815e-09 2.047443e-07
-
-550        Mir132    106.46062 2.691980e+01 1.860014e+02 6.909467e+00       2.788574 1.329950e-08 3.161402e-07
-
-76  2610203C20Rik     79.17666 1.649993e+01 1.418534e+02 8.597210e+00       3.103869 1.594438e-08 3.712764e-07
-
-540     Mir125b-1     79.01988 1.649993e+01 1.415398e+02 8.578206e+00       3.100676 1.650666e-08 3.766821e-07
-
-# VOOM top 50
-
-                ID      logFC    AveExpr          t      P.Value    adj.P.Val         B
-
-600         Mir192  -6.948883 14.6763803 -42.722954 2.301199e-16 2.625668e-13 27.266471
-
-536        Mir122a -10.426125  8.1698641 -21.722912 2.859682e-12 1.087633e-09 17.760171
-
-568         Mir149   7.030463  6.3160807  20.883835 4.915491e-12 1.402144e-09 17.277609
-
-645        Mir208a  11.015018  3.9395538  23.252407 1.118938e-12 6.383542e-10 17.208662
-
-530         Mir10b   5.130915 12.2628672  18.242023 3.124991e-11 4.963978e-09 16.221503
-
-561       Mir143hg   2.249221 16.2444825  18.082481 3.521739e-11 4.963978e-09 16.026695
-
-560         Mir143   2.251067 16.2358599  18.081481 3.524391e-11 4.963978e-09 16.026084
-
-646        Mir208b  12.433228  4.6076218  19.592458 1.179199e-11 2.690931e-09 15.683666
-
-523        Mir101b  -3.765722 10.8508440 -16.538566 1.180419e-10 1.036045e-08 14.900027
-
-796         Mir499  11.567529  3.7874598  17.942086 3.915496e-11 4.963978e-09 14.821741
-
-566        Mir148a  -2.638213 15.4435820 -16.548188 1.171186e-10 1.036045e-08 14.814792
-
-844         Mir802  -9.158434  2.9157675 -17.316522 6.338616e-11 7.232360e-09 14.381577
-
-698        Mir3073  -8.420542  2.5457189 -16.702657 1.033066e-10 1.036045e-08 13.985845
-
-649          Mir21  -2.938537 13.1642917 -15.375404 3.148335e-10 2.394833e-08 13.867698
-
-585        Mir181c   3.742560  9.6295577  15.242361 3.537063e-10 2.522368e-08 13.810405
-
-791         Mir490   8.474378  3.7506957  16.259650 1.484816e-10 1.210125e-08 13.424617
-
-663         Mir23a   3.165768  8.7896592  14.631179 6.110682e-10 3.873493e-08 13.269174
-
-586        Mir181d   3.636211  6.3713218  14.317073 8.157508e-10 4.898798e-08 12.956333
-
-642         Mir204   7.684425  4.7751735  15.033484 4.254268e-10 2.855364e-08 12.822427
-
-671         Mir27a   3.106935  9.9255796  13.838251 1.281011e-09 6.960160e-08 12.513086
-
-552        Mir133b   6.493549  1.2544862  13.969968 1.129934e-09 6.446275e-08 11.982684
-
-608       Mir194-2  -5.264136  6.0897615 -13.044012 2.792884e-09 1.448491e-07 11.715753
-
-616         Mir195   3.216595  7.4509350  12.869478 3.332788e-09 1.653353e-07 11.587523
-
-756         Mir378   3.097393  7.3832049  11.684163 1.171371e-08 5.346138e-07 10.329692
-
-672         Mir27b   1.976376 15.0957731  11.756036 1.082197e-08 5.144946e-07 10.127719
-
-1017      Snord104  -2.337374 10.6109024 -11.495675 1.444482e-08 6.339052e-07 10.023395
-
-722         Mir322   3.296618  8.2153415  11.415362 1.580762e-08 6.441605e-07 10.008472
-
-655         Mir215   3.045873  5.7544234  11.148134 2.141822e-08 8.082459e-07  9.753268
-
-628        Mir1983   5.895500  0.9931851  11.445812 1.527548e-08 6.441605e-07  9.749260
-
-344         Dnm3os   3.363344  5.8607432  11.092261 2.283960e-08 8.082459e-07  9.689496
-
-637        Mir200a  -6.191561  1.7981309 -11.322172 1.756229e-08 6.909853e-07  9.662295
-
-587         Mir182  -4.903995  7.1511683 -11.074468 2.331304e-08 8.082459e-07  9.658842
-
-582      Mir181a-2   3.048298  6.9414651  11.072128 2.337609e-08 8.082459e-07  9.644017
-
-614        Mir1948  -7.195525  4.5513493 -11.005492 2.524936e-08 8.473388e-07  9.341794
-
-654         Mir214   3.280874  5.4784451  10.768257 3.332555e-08 1.086413e-06  9.318504
-
-571         Mir153   5.963803  1.4386315  10.727082 3.498742e-08 1.093990e-06  9.035569
-
-318        Cyp3a25  -6.318200  1.4888933 -10.698226 3.620443e-08 1.093990e-06  9.024973
-
-464         Gm5441   5.982176  1.4484953  10.692891 3.643436e-08 1.093990e-06  9.000362
-
-541      Mir125b-2   3.077678  7.4316058  10.446668 4.893073e-08 1.431538e-06  8.884250
-
-551      Mir133a-1   5.144671  0.5903264  10.358205 5.447229e-08 1.553822e-06  8.575535
-
-550         Mir132   2.847559  5.3211839  10.110952 7.380297e-08 2.004981e-06  8.531491
-
-13   1110038B12Rik  -2.226702 10.8487089 -10.194609 6.655312e-08 1.852125e-06  8.439308
-
-922        Rabggtb  -1.935779  9.9874171  -9.928995 9.262821e-08 2.457879e-06  8.133384
-
-569         Mir150   2.938531  7.6297870   9.842102 1.033602e-07 2.620755e-06  8.116464
-
-800         Mir504   5.256127  0.6221088   9.892894 9.693595e-08 2.513725e-06  8.068853
-
-573         Mir155   3.906600  3.9899000   9.732173 1.188627e-07 2.712448e-06  8.046518
-
-666        Mir24-2   2.833979  7.3083691   9.767192 1.136724e-07 2.646944e-06  8.030550
-
-700      Mir3074-2   2.833979  7.3083691   9.767192 1.136724e-07 2.646944e-06  8.030550
-
-664         Mir23b   2.124129  9.8141190   9.806316 1.081569e-07 2.625681e-06  7.979464
-
-631        Mir199b   5.752816  2.8805143   9.823920 1.057683e-07 2.623514e-06  7.979387
-
-Warning messages:
-
-1: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group ==  :
-
-  Outlier (-Inf) in boxplot 5 is not drawn
-
-2: In bplt(at[i], wid = width[i], stats = z$stats[, i], out = z$out[z$group ==  :
-
-  Outlier (-Inf) in boxplot 7 is not drawn
-
-3: In bxp(list(stats = c(-Inf, -Inf, -0.158608221176912, 0.826586442285183,  :
-
-  some notches went outside hinges ('box'): maybe set notch=FALSE
-
-4: In par(defpar) : calling par(new=TRUE) with no plot
-
-R version 2.15.1 (2012-06-22)
-
-Platform: x86_64-unknown-linux-gnu (64-bit)
-
-locale:
-
- [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C               LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8     LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8    LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       
-
-attached base packages:
-
-[1] methods   grid      stats     graphics  grDevices utils     datasets  base     
-
-other attached packages:
-
- [1] edgeR_3.0.8        limma_3.14.4       DESeq_1.10.1       lattice_0.20-15    locfit_1.5-9.1     Biobase_2.18.0     BiocGenerics_0.4.0 gplots_2.11.0      MASS_7.3-23        KernSmooth_2.23-10 caTools_1.14       gdata_2.12.0.2     gtools_2.7.1       stringr_0.6.2     
-
-loaded via a namespace (and not attached):
-
- [1] annotate_1.36.0      AnnotationDbi_1.20.7 bitops_1.0-5         DBI_0.2-7            genefilter_1.40.0    geneplotter_1.36.0   IRanges_1.16.6       parallel_2.15.1      RColorBrewer_1.0-5   RSQLite_0.11.3       splines_2.15.1       stats4_2.15.1        survival_2.37-4      XML_3.96-1.1         xtable_1.7-1        
-
-</pre>
-
-<hr/><div class="infomessage">This tool (edgeR) was generated by the <a href="https://bitbucket.org/fubar/galaxytoolfactory/overview">Galaxy Tool Factory</a></div><br/>
-</div></body></html>
-

--- a/rgedgeR/test-data/edgeRtest1out.xls	Sat Jul 27 22:28:00 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1142 +0,0 @@
-Name	logFC	logCPM	LR	PValue	adj.p.value	Dispersion	totreads	case_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam	case_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam	case_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam	case_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam	control_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam	control_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam	control_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam	control_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam	case_X11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam	case_X11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam	case_X11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam	case_X11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam	control_X11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam	control_X11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam	control_X11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam	control_X11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam
-Mir122a	-10.6613482198735	12.5379487184339	445.912028851371	5.59474310450852e-99	6.38360188224422e-96	0.102055096028295	90428	6.64466912039531	2.86464823551992	20.1236936368881	4.75652253016081	20841.6623198401	16818.9531619257	7242.55663282834	8468.31297344994	12	7	27	8	29767	24233	11911	24463
-Mir192	-7.10901851688288	17.2474145508888	366.131659138235	1.3015583263717e-81	7.42539025195057e-79	0.0776548700185199	2325567	1779.66387941254	1294.41176699279	4493.54625691845	1933.52640851037	463599.032378899	340312.253828562	383591.60517699	182292.180510107	3214	3163	6029	3252	662133	490327	630849	526600
-Mir208b	13.4237202575152	9.82233816515324	355.417815392181	2.80129611458365e-79	1.06542628891331e-76	0.124440587141633	14756	1245.90702213628	570.139045385768	4930.34448733332	881.902421077918	0.74532198655141	0	0	0	2049	1647	8904	2155	1	0	0	0
-Mir208a	11.9775863683342	8.38828977985358	348.815401742963	7.675450754893e-78	2.18942232783323e-75	0.0993679816515115	4638	433.789589950159	712.527819143148	1006.59908044528	649.748467524829	0	0	0	0.553722426699609	1060	956	1693	928	0	0	0	1
-Mir499	14.4882160574998	8.61277040381698	291.127944921827	2.82350748745294e-65	6.4432440863676e-63	0.134816198797062	6527	608.439028317971	506.657690265579	2521.60879492395	270.357373677161	0	0	0	0	869	730	4147	781	0	0	0	0
-Mir149	6.86973108218652	8.78566474384905	253.019861795716	5.70293016120625e-57	1.08450721898939e-54	0.0983468375157501	6164	774.657674952754	459.571424069838	1710.51395913549	766.394692672161	17.5039996639232	6.24646467450714	4.86444908593961	5.5386913941544	1399	1123	2295	1289	25	9	8	16
-Mir490	8.4539298899245	6.90959613094456	251.056095815646	1.52828085290668e-56	2.4910977902379e-54	0.0974500488770791	1741	209.881556643346	217.749755819205	520.538722875595	195.794075709069	1.03850463640395	0.553722426699609	0	0.74532198655141	353	311	750	322	3	1	0	1
-Mir802	-12.4996776940066	6.62939088571757	237.561606597444	1.33781241656995e-53	1.90805495913289e-51	0.10939980863872	1514	0	0	0	0	305.654779538184	164.10342034907	155.772295189245	209.286991327076	0	0	0	0	552	401	209	352
-Mir204	7.37117920479641	7.55899555710097	237.12302218121	1.66736458270285e-53	2.11384776540439e-51	0.10292005004102	2601	425.578854320855	326.416358632286	646.247667592045	375.481932100929	3.04028067871226	0.6923364242693	0.553722426699609	3.68311915995418	571	549	923	541	5	2	1	9
-Mir1948	-7.58332571104735	7.29345576009458	204.796406017043	1.87589722530299e-46	2.14039873407072e-44	0.118339985035871	2404	1.2161122714849	0.6923364242693	1.66116728009883	1.63694184886853	647.684806313175	385.278324943026	181.341436518244	428.229856018989	2	2	3	4	869	648	259	617
-Mir3073	-11.7485555893732	5.88146234349958	200.033500954155	2.05362547312175e-45	2.13016969530174e-43	0.110685621278186	904	0	0	0	0	207.347142288176	75.4646702453536	72.5376378976488	87.5763889144661	0	0	0	0	341	218	131	214
-Mir194-2	-5.43982669183809	7.86004832737241	165.572392495399	6.85919857312405e-38	6.52195464327879e-36	0.106710199302315	3570	10.5207261072926	6.13853193325697	14.9064397310282	9.51304506032163	921.410542308918	600.354660383186	266.936643590936	304.628026678492	19	15	20	16	1316	865	439	880
-Mir10b	5.0328982107069	13.880769769219	160.065802570007	1.0946399286548e-36	9.60757045073175e-35	0.107954343937396	197340	25838.8226297643	32163.6053489474	36317.2985027079	34465.2158674084	1825.38451949884	373.861669105422	658.375965345836	727.211416359842	34668	54096	51870	49658	3002	1080	1189	1777
-Mir101b	-3.92528713393055	11.9360901455378	120.624266541894	4.61814317471517e-28	3.76378668739286e-26	0.0966307527814339	59019	219.816814705503	301.225000124588	811.923157038789	427.069498293958	10145.0679915167	7747.97041123897	11280.4211505294	6628.41993572847	635	544	1984	573	17063	11066	16253	10901
-Mir182	-5.24438373094747	8.94270765623571	118.928149724545	1.08592583416118e-27	8.26027584518606e-26	0.149934428671101	7189	16.9622423945978	14.3967830941898	22.0987149597251	31.3035234351592	984.005598427018	615.44062818354	2366.0220083772	653.660345923136	49	26	54	42	1655	879	3409	1075
-Mir200b	-6.72534784619757	5.76518685294719	115.731891447532	5.44098879544178e-27	3.88010513474942e-25	0.167124904530932	888	2.43222454296981	0	1.66116728009883	0	369.679705329499	97.5087118682966	46.2105591127573	107.578002727623	4	0	3	0	496	164	66	155
-Mir181c	3.6118671281253	10.5698150360209	107.820107113202	2.94315295097335e-25	1.97537501003564e-23	0.0938527006387662	23605	2420.85208718677	1892.87875056625	4093.0929402801	1902.59025813986	232.036507077113	272.787847077816	228.313081447719	298.968314259808	3488	3113	11824	3436	567	366	384	427
-Mir181d	3.48997562250607	7.2320639569436	102.186614268585	5.05301947727886e-24	3.20305290198621e-22	0.087384984044046	2139	310.053946405387	202.152207531835	539.823349635392	295.665994593338	36.4833681445471	14.5390649096553	25.471231628182	15.550947564251	416	340	771	426	60	42	46	38
-Mir21	-3.07777147203033	13.8815003666918	91.3732407445455	1.1897452302054e-21	7.14473319823348e-20	0.0849427206355669	229120	3207.21258454416	2190.82625708005	4348.9112490476	2010.56613134628	27154.0006244933	33227.944804435	25707.2205795704	35379.0841207216	4621	3603	12563	3631	66353	44582	43237	50530
-Mir199b	5.41147631803522	4.69586911909022	86.7037178851385	1.26059609329233e-20	7.19170071223273e-19	0.156561826531982	370	43.4032680877174	44.8102391396434	99.2493831616134	49.2525469951386	1.3846728485386	0.553722426699609	0	2.98128794620564	73	64	143	81	4	1	0	4
-Mir193	-5.36015662788668	4.77547692611212	84.6612650026128	3.5412053458764e-20	1.92405490459285e-18	0.155464968416992	421	1.49064397310282	1.1891306325402	2.80063994622771	0.694051630500793	101.545374668989	34.9629894255996	33.7770680286762	33.9665433640219	2	2	4	1	167	101	61	83
-Mir23a	3.00307076424737	9.46741956688047	82.28684490401	1.17702908493873e-19	6.10450084506861e-18	0.0892034490333833	10118	1149.88932166638	1127.95773834321	2471.51785621332	1096.32521274364	150.583172278573	126.802435714211	89.2133307633346	243.720289602311	1934	1611	3561	1803	435	229	218	327
-Mir195	3.06054621394571	8.15279745103936	81.3972715690713	1.84612638492429e-19	9.15839219651573e-18	0.0913301572784805	3962	429.134880692197	283.190939854255	922.708619350646	470.89573048592	110.625277875995	77.7337826160888	45.6042101806839	41.540185456158	775	692	1238	792	158	112	75	120
-Ahsg	-10.1013431702234	6.6385887851201	79.821328032349	4.09844702296257e-19	1.92375926690416e-17	0.42092199405061	1524	0	0.553722426699609	0	0	348.415275334279	12.6028797580247	610.071383210197	24.3222454296981	0	1	0	0	586	18	879	40
-Mir148a	-2.78937502090353	16.047168680842	79.7658888859378	4.21507288979878e-19	1.92375926690416e-17	0.0819605364404836	1002397	15925.5982512306	8528.20007414923	22070.8222058197	10590.1952912549	192723.868638491	105445.564275186	179549.727112645	134274.698694836	26191	24636	39859	25878	258578	177349	256441	193465
-Dnm3os	3.18944316253823	6.61883431628908	79.1961422287326	5.62397892398994e-19	2.46806152010482e-17	0.0949653148790185	1401	134.000827261305	87.167153452249	365.207773410191	182.531552094921	37.1084792875172	24.9858586980285	12.161122714849	13.846728485386	242	213	490	307	53	36	20	40
-Mir27a	2.92177170736328	10.5812768795259	77.2698776994316	1.49123094631961e-18	6.30183151759511e-17	0.0912505912483571	21886	2383.61235292684	2512.17403176626	5321.98790268008	2361.69003122368	328.513633315783	347.737683967355	163.694184886853	566.444709779072	4009	3588	7668	3884	949	628	400	760
-Mir429	-5.34193377949947	4.95110312707712	76.3875799779135	2.33112791050646e-18	9.49934623531384e-17	0.183241171201345	499	1.7836959488103	0.700159986556928	2.08215489150238	1.82416840722736	91.7345762156822	45.405238989368	16.7786539509024	75.2775206416924	3	1	3	3	265	82	41	101
-Mir214	3.12590636489108	6.20234665031187	74.2821251599606	6.77138706168541e-18	2.66419056461485e-16	0.0953276171520653	1048	110.058160569384	56.4254185779479	198.23262875846	93.7149208477231	33.5394893948135	15.4586982230226	11.9027197714678	20.127497284523	181	163	358	229	45	26	17	29
-Mir200a	-7.59226302352062	4.05994320136271	73.7142550533581	9.02845045111825e-18	3.43382065490864e-16	0.224178202729185	264	0	0	0.594565316270102	0	90.2267119651031	32.2269751943499	11.4235510004434	26.0249540548816	0	0	1	0	130	53	33	47
-Mir194-1	-3.97021853073367	5.39389876933198	73.2237979529499	1.1575165879669e-17	4.26040782861365e-16	0.130958864780352	635	3.56739189762061	9.10207982524007	5.55241304400634	3.64833681445471	76.1570066696229	88.5955882719375	33.1480724395876	105.090400103749	6	13	8	6	220	160	81	141
-Mir378	2.95431952960146	8.05336780578876	73.0964650986627	1.23465451887634e-17	4.40231501886846e-16	0.0956665499194766	4075	425.697271826612	392.139171232948	1155.9147140464	188.315507401249	76.4136948845461	36.8311915995418	91.6746043458234	63.0239235246308	608	565	1901	544	138	90	123	106
-Mir322	3.05856921521976	8.94824187288921	72.8372126855238	1.40796901194656e-17	4.86815952312432e-16	0.103656954331831	7074	1012.89257972337	671.858807385215	1784.70780573361	855.071608776977	158.70265142878	78.9263523667001	50.3887408296645	91.6687435366374	1359	1130	2549	1232	261	228	91	224
-Mir215	2.90893351586836	6.38192368892387	70.311049912704	5.06531683728474e-17	1.69986073862997e-15	0.0900203619873792	1182	123.075020467911	161.036796908093	272.762290786812	122.219283284233	19.3854198795404	17.1653952276879	11.4585929420797	26.8315915158508	207	230	393	201	56	31	28	36
-Cyp3a25	-9.77860211373653	3.91325729596345	70.0264241191466	5.85153294977192e-17	1.90759974162565e-15	0.264452365698728	226	0	0	0	0	56.6444709779072	17.836959488103	65.1148787497943	18.7393940235214	0	0	0	0	76	30	93	27
-Mir183	-4.21446206828232	5.24792871814947	66.3110130402762	3.85100994568175e-16	1.22055620778413e-14	0.159551640795599	563	8.40191983868314	1.38810326100159	2.43222454296981	2.42317748494255	86.3806985651391	29.0557178174163	134.903279565805	77.2934911151132	12	2	4	7	156	71	181	130
-Mir181a-2	2.83771284942958	7.57379761415609	65.529002601634	5.72650030707276e-16	1.76592887847838e-14	0.0983402987214175	2817	288.826664477665	137.774948429591	639.549402838049	182.109780686623	58.13511495101	41.025006822637	80.5183984540467	56.912233701065	475	398	1155	445	78	69	115	82
-Mir155	3.73430977551283	4.97536414314019	65.0759982171349	7.20644948975499e-16	2.16383128100275e-14	0.13295454756028	463	33.9665433640219	58.8804369375614	114.156540723859	52.5119989917696	9.7167228270111	1.82416840722736	2.7693456970772	4.98350184029649	83	79	192	75	14	3	8	9
-Snord91a	-2.81834162418986	6.5922507494912	64.2934517703521	1.07201440082266e-15	3.13632931112474e-14	0.0942244574316978	1437	13.846728485386	16.0579503742887	33.1480724395876	18.6330496637853	215.827209806047	179.240956558574	248.470483719284	173.295998686599	40	29	81	25	363	256	358	285
-Mir125b-2	2.85223280857829	8.08109324518757	64.2082166292202	1.11940933259702e-15	3.19311512123301e-14	0.10276577547371	3837	315.520541369408	440.485294051883	763.42186609081	485.210870683951	108.272054358124	90.6003642256253	20.770092728079	73.6450827510481	771	591	1284	693	156	149	60	133
-Serpina4-ps1	-10.0905640887531	4.22405077630453	64.0209367290974	1.23103990147691e-15	3.4258939697199e-14	0.344064523917905	295	0	0	0	0	108.071688049954	11.2967410091319	81.9187184271606	9.7167228270111	0	0	0	0	145	19	117	14
-Mir133b	9.29339239795832	3.40470370765963	63.5957583468182	1.52757738622221e-15	4.14991856590367e-14	0.264043920283644	159	17.7191176543875	10.6401220176454	57.3897929644586	14.2695675904824	0	0	0	0	32	26	77	24	0	0	0	0
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-Mir3470b	-4.68838941248773	3.14503107104778	30.9125299029967	2.69923440880683e-08	3.24192258994589e-07	0.327784732956504	132	0	2.37826126508041	0	0	27.9705822441528	9.34654172763554	19.9340073611859	7.77547378212549	0	4	0	0	46	27	36	19
-Mirlet7e	1.8538118650749	6.68153082866704	30.3142211972717	3.67422135731732e-08	4.36696517572819e-07	0.0957747301343719	1576	163.137276867764	111.048260880127	394.020375961109	67.8489695783913	63.1243566437555	31.101895128502	47.7006071392902	50.5380518829586	233	160	648	196	114	76	64	85
-Mir592	-5.63358152644221	2.20162078005207	28.718229340558	8.371201918502e-08	9.84694988557813e-07	0.343558801214923	70	0.34616821213465	0	0	0	16.6478288555628	10.5023997983539	5.55241304400634	10.9450104433641	1	0	0	0	28	15	8	18
-Terc	-5.58351159909917	2.14826836122565	28.6530965218399	8.65754423415898e-08	1.0079855072628e-06	0.331287016798336	66	0.694051630500793	0	0	0	9.00318016877689	13.4157957579254	5.94565316270102	10.5023997983539	1	0	0	0	22	18	10	15
-Mir547	7.57267023512074	1.64822521108977	28.171949268209	1.1100167882359e-07	1.27932237916885e-06	0.423621435325724	42	8.30583640049414	3.27388369773705	7.4532198655141	5.35108784643091	0	0	0	0	15	8	10	9	0	0	0	0
-Scnn1b	7.66141003593485	1.74267962711525	28.1236474183351	1.13806765009286e-07	1.28672413942851e-06	0.453880174551202	45	13.8810326100159	3.04028067871226	3.80785033348115	4.98350184029649	0	0	0	0	20	5	11	9	0	0	0	0
-Snord72	-1.99865753766157	5.32762717247088	28.1113796190191	1.14530448260111e-07	1.28672413942851e-06	0.108944101046975	603	11.6281709606918	9.82165109321115	42.4833532334304	9.51304506032163	111.325437862552	70.7932663110809	74.7909046963216	34.9629894255996	21	24	57	16	159	102	123	101
-Proc	-8.34060291685597	2.47353428644525	28.1030061666675	1.15027048397641e-07	1.28672413942851e-06	0.623270866998637	83	0	0	0	0	19.4334456540222	1.2161122714849	17.3084106067325	1.66116728009883	0	0	0	0	28	2	50	3
-Mir145	1.82731571180131	9.10812234302671	27.143112773632	1.88937088461262e-07	2.09298269839126e-06	0.109850081363838	7539	447.941666502237	664.466912039531	651.093620387456	1175.37277279157	419.168547970422	308.070394085048	157.54972012368	307.068348549938	1294	1200	1591	1577	705	440	227	505
-C430049B03Rik	1.71016972066493	10.8223091327111	26.8082784375072	2.24672814113162e-07	2.46492000868383e-06	0.0988498324160551	25716	1536.29452545358	2029.94641628077	2948.95074073665	2969.36279442082	1186.75237127512	1158.06461776516	571.898543532653	1184.4933524263	4438	3666	7206	3984	1996	1654	824	1948
-Taf1d	-1.76454724951041	6.55908754578095	26.4166122241945	2.75163761899181e-07	2.99011287930443e-06	0.0995348557652302	1421	31.5119617623154	39.208959247188	108.272054358124	32.8350313300924	123.58205173207	96.3477022457321	139.549292616042	171.424056906824	53	56	156	54	357	174	341	230
-Mir144	2.42421663401894	10.1128061755165	26.3134903354097	2.90254150898289e-07	3.12433949221649e-06	0.192587788459561	13709	2856.81917445155	1437.06436942484	735.167985884775	2622.127060032	439.624586141793	162.006723279016	184.38956809097	453.023656674364	3833	2417	1050	3778	723	468	333	1107
-Mir3074-1	2.96242426446157	3.71009425877681	26.2448795961817	3.00751187649521e-07	3.20707574867386e-06	0.213306639112716	189	11.4235510004434	14.3967830941898	28.2372468929821	29.067557475505	2.97282658135051	4.9011199058985	4.16430978300476	2.43222454296981	33	26	69	39	5	7	6	4
-Mir24-1	2.96234295411287	3.71014414709217	26.1322229529753	3.18818831899091e-07	3.36826191848947e-06	0.214482793171814	189	22.9037038065262	15.8094595293037	23.8856066372908	21.5951746412848	2.04617731108566	5.21725390585987	3.56739189762061	2.80063994622771	33	26	69	39	5	7	6	4
-Mir30e	1.71360301527884	13.5591451347018	25.7546472841332	3.8769235297702e-07	4.05832086923651e-06	0.103612748827971	186796	17504.6321761464	12414.5238037197	53758.2837678409	15420.4391264666	9640.12197606083	3715.07725262906	2984.5638799109	4688.20145515946	23486	20880	76780	22218	15854	10732	5390	11456
-Mir488	4.56803366042882	2.3917189958476	25.1907233635027	5.19313914653799e-07	5.38670160563623e-06	0.365626941485075	78	15.8094595293037	2.0770092728079	18.8265625077867	3.68311915995418	0.74532198655141	0.594565316270102	0.700159986556928	0	26	6	34	9	1	1	1	0
-Mir100	1.94757024837894	9.41024940137313	25.0279123677811	5.65063511960147e-07	5.80844564996872e-06	0.134729292386691	8837	1553.28754906077	924.245326328527	415.40185456158	968.460524297617	283.600175316472	421.852244388098	159.343504760387	422.196471893828	2238	1520	1200	1749	693	566	268	603
-Mir1a-1	7.31088930452147	1.41799634478391	24.9750177157778	5.80779933821914e-07	5.91669557581075e-06	0.451973173766053	42	2.98128794620564	2.97282658135051	16.8038396773663	6.24646467450714	0	0	0	0	4	5	24	9	0	0	0	0
-Mir301	1.57184329832823	7.17626052524146	24.0252804396516	9.50790943501817e-07	9.60046430562454e-06	0.0899167531497226	2119	195.611989052863	186.242556424143	461.544334283027	182.416840722736	67.8489695783913	66.4466912039531	36.0127206751076	115.524907915469	329	266	665	300	196	120	88	155
-Dcaf11	-4.78953443264601	2.83644144356938	23.7635451621341	1.0892609656454e-06	1.08484575916239e-05	0.455818602256535	105	0.409235462217131	0.74532198655141	0	0.700159986556928	21.5156005455246	3.64833681445471	19.731588091675	4.42977941359688	1	1	0	1	31	6	57	8
-Eci2	-8.06753534827286	2.20028041533708	23.7562404618698	1.09340282474737e-06	1.08484575916239e-05	0.726538151382684	69	0	0	0	0	13.8430606674902	1.22770638665139	30.5582014486078	0	0	0	0	0	25	3	41	0
-2610019E17Rik	-1.76498715582456	5.88698153478579	23.6108108113204	1.17923139294727e-06	1.15991639599383e-05	0.107886602411712	892	24.9175092014824	9.00318016877689	64.0976908434213	24.9717432833443	173.639676666118	136.034119578155	59.5895013027603	53.6560728808707	45	22	86	42	248	196	98	155
-Mir99b	2.10284909354602	11.4525971851371	23.5299564012735	1.22983936424459e-06	1.19674926232621e-05	0.16629271885375	35086	7216.54898144226	4631.40653033179	1703.16523621461	2518.71991149171	1407.56240867041	825.427927291954	842.959166789645	1390.68827475577	10307	6673	2801	7276	2542	2017	1131	2339
-Sqrdl	-5.41742806471114	2.76474110616331	23.5177682272925	1.23765480240572e-06	1.19674926232621e-05	0.561839947505073	102	0.34616821213465	0	0.409235462217131	0	20.8097860694536	2.80063994622771	40.254994569046	1.82416840722736	1	0	1	0	35	4	58	3
-Mir212	2.63108555364757	4.02020066871904	23.2608792504594	1.41448044421687e-06	1.34873799676087e-05	0.207180817475692	232	37.8086392740741	23.597755437027	44.9961540449414	12.1158874247127	7.19839154709492	1.63694184886853	2.98128794620564	8.32391442778142	54	34	74	35	13	4	4	14
-Mir181b-2	3.40040902354404	3.25344412533602	23.2554489052629	1.41847992647944e-06	1.34873799676087e-05	0.30032007920964	154	9.96700368059297	6.95700285769123	65.5883348165241	11.2967410091319	1.40031997311386	0.694051630500793	3.04028067871226	1.3846728485386	18	17	88	19	2	1	5	4
-Mir92-1	-1.42313874127891	13.2572416738784	23.1627136686375	1.48855771403684e-06	1.40367301794714e-05	0.0807518678586245	145450	3039.80101334885	4986.20409002893	9608.77007624111	5538.2654936653	22431.7486977856	14704.013474524	8604.01091260672	14343.6257412267	7428	6690	16161	7910	32320	24182	24855	25904
-Mir17hg	-1.42315386804028	13.2572524918731	23.0652749733229	1.56593452715518e-06	1.46453384875743e-05	0.0810949536849217	145451	2571.33747973618	3704.40303462039	6613.65430489106	5895.49691362165	19216.3510218497	16931.2687949196	17251.3473277277	15751.0861402725	7428	6690	16161	7910	32320	24182	24856	25904
-Atf5	-7.60443813911671	1.74151085310353	22.8864484686282	1.71859237722938e-06	1.59423894505587e-05	0.604880887600787	50	0	0	0	0	10.3369543076217	0.34616821213465	14.9505055208895	2.04617731108566	0	0	0	0	17	1	27	5
-Snord4a	-1.6940423087756	6.22260127860836	22.8611154654003	1.74139329273598e-06	1.60236269920302e-05	0.105509716106031	1151	27.6861213349805	15.9601830264681	115.524907915469	18.4315248043731	226.851835644445	136.034119578155	100.329262397505	66.1181285177181	50	39	155	31	324	196	165	191
-Gm10768	-7.79734408694512	1.93534753760022	22.7413703227339	1.85334549881566e-06	1.69173377131893e-05	0.684190381270136	59	0	0	0	0	10.6401220176454	0	17.2423941718329	2.80063994622771	0	0	0	0	26	0	29	4
-Mir700	2.97881955365179	3.77125098123284	22.3973004682007	2.21685386438204e-06	2.00748433274596e-05	0.266009663645126	177	22.4051195698217	35.3966331555404	18.849740208016	13.846728485386	2.76861213349805	2.45541277330279	1.49064397310282	5.94565316270102	32	51	31	40	5	6	2	10
-Rpph1	-2.08314841010585	4.82399815840611	22.1362656517284	2.53966388950891e-06	2.2715144267454e-05	0.148476093177056	430	7.4532198655141	8.91847974405152	28.0063994622771	10.4107744575119	76.0070169678065	16.6160741824632	57.0334099500598	30.2834242040677	10	15	40	15	125	48	103	74
-Snord45c	-1.60898685331134	6.56442093351196	22.129796052749	2.54823704314997e-06	2.2715144267454e-05	0.100094766607824	1427	39.9091192337449	34.0085298945389	115.530665791066	21.4624291523483	178.852343823974	86.7579179900318	239.993679669554	126.047847049262	57	49	190	62	323	212	322	212
-Snord16a	-2.75004105989817	4.5628099378298	22.0776507411564	2.61840576298403e-06	2.31596974849983e-05	0.254607325505457	368	3.47025815250396	3.04028067871226	10.0388781519048	4.98350184029649	55.6560228615299	17.8877276772338	77.2934911151132	21.0047995967078	5	5	29	9	136	24	130	30
-0610005C13Rik	-4.61110527397388	3.09169695040067	21.7924212667961	3.03797783111965e-06	2.66640977331348e-05	0.511147066071314	126	0	1.2161122714849	0	1.10744485339922	16.3694184886853	4.47193191930846	41.6195721389071	4.20095991934157	0	2	0	2	40	6	70	6
-Mtmr2	2.05482556337216	5.2110171425161	21.6657160211323	3.24540066900051e-06	2.82671920864854e-05	0.154685834812798	580	39.8358761900968	49.7113590455419	191.558250018219	37.0914242802896	6.92336424269299	8.30583640049414	17.5971248753366	20.1236936368881	67	71	276	61	20	15	43	27
-Cyp2d13	-7.38060767609528	1.52270708191277	21.2011219028663	4.13522383125616e-06	3.57446241777521e-05	0.607831105280726	44	0	0	0	0	10.5207261072926	0.409235462217131	14.9064397310282	2.37826126508041	0	0	0	0	19	1	20	4
-Mir5109	-2.75158274518898	6.32573307152633	20.9782259766441	4.64532969759298e-06	3.98520389846135e-05	0.29431582377148	1282	10.0388781519048	6.64466912039531	43.3789589950159	17.1424056906824	325.821793316016	28.0063994622771	331.756679379379	27.9705822441528	29	12	106	23	548	40	478	46
-Tmem205	-4.45172142322718	2.82863094255824	20.7479224478071	5.23883837763376e-06	4.46083178274636e-05	0.496107622810268	106	1.2161122714849	0	0.553722426699609	0.409235462217131	26.0862695292994	2.37826126508041	39.9091192337449	4.16430978300476	2	0	1	1	35	4	57	6
-Mir1943	2.47773115878141	3.93902294197728	20.6772296647227	5.43586018224117e-06	4.59430849476828e-05	0.207434900508124	215	30.5582014486078	23.188047334534	44.1100791530865	25.6799103285293	4.86444908593961	2.7693456970772	2.21488970679844	6.13853193325697	41	39	63	37	8	8	4	15
-1810032O08Rik	-1.61479478539896	5.72442513671048	20.5949001224573	5.67470818799052e-06	4.76091326654205e-05	0.10320089154802	801	16.6116728009883	15.9601830264681	69.3149447492811	17.836959488103	159.63647693498	116.600673924133	67.4942310674121	35.3091576377343	30	39	93	30	228	168	111	102
-Mir292	-7.19606685964968	1.35004623222957	20.3159318474763	6.5651643128287e-06	5.46777553353105e-05	0.584148616914066	41	0	0	0	0	15.2014033935613	2.7693456970772	0.553722426699609	2.86464823551992	0	0	0	0	25	8	1	7
-Gas5	-1.39482444939415	10.688269847049	20.1001588571361	7.34905714139414e-06	6.07628565096429e-05	0.0892063812051997	24887	521.775214326843	746.067308537961	2006.65794241159	835.991023948972	3962.34075852903	2343.44834715141	1593.06611224366	2146.78184831439	1275	1001	3375	1194	5709	3854	4602	3877
-Snord33	-1.42230425294518	7.89285295942678	19.9614960825249	7.90174242598409e-06	6.4862504374445e-05	0.0908019923476473	3442	140.865855458217	115.94023667267	217.049595832648	131.869809795151	394.628432096851	207.008590856521	392.589200530023	246.359748254713	189	195	310	190	649	598	709	602
-Mir30d	1.42700409137036	13.3849319697309	19.6539753184979	9.28100238045923e-06	7.56401694007427e-05	0.0956896506480022	161730	14448.7668437655	11465.5064955597	19920.5959355006	11036.2416865499	6561.27216572727	8118.04707751796	3478.20710018009	8264.68848131798	20818	18856	57546	19931	16033	10892	5850	11804
-AW495222	-6.16544234758806	2.74819064610763	19.5961315313439	9.56626965541824e-06	7.74121537363987e-05	0.83637505410564	101	0	0	0	0.594565316270102	25.2057595160494	0	38.3075365517745	0.34616821213465	0	0	0	1	36	0	63	1
-Gm6307	4.40591164343186	1.72334399482617	19.0765857608822	1.25576112752235e-05	0.000100903059612887	0.411047879493315	52	4.20095991934157	4.16430978300476	17.6336279365311	3.11551390921185	0	0	0	1.1891306325402	6	6	29	9	0	0	0	2
-Mir466f-3	-3.79728830821604	3.13167479897481	18.7586994191299	1.48345100740014e-05	0.000118364867093955	0.461197855860477	134	0.6923364242693	0.553722426699609	1.22770638665139	1.49064397310282	31.5119617623154	2.80063994622771	43.72525272155	3.64833681445471	2	1	3	2	53	4	63	6
-Snord96a	-1.82073221921608	4.9953501700774	18.3396893905852	1.84816467912299e-05	0.00014644138186662	0.142009104156823	487	9.51304506032163	15.4035197042524	38.8668913080444	7.29667362890942	50.1943907595242	39.3142922956723	43.3789589950159	43.9739972065332	16	22	56	12	145	71	106	59
-Mir137	-6.77715938723149	0.926461536550918	18.2559426818403	1.9312249605068e-05	0.000151967426202639	0.519868670969044	29	0	0	0	0	7.72934911151132	5.60127989245543	1.38810326100159	3.64833681445471	0	0	0	0	13	8	2	6
-Mir181b-1	6.40713612447329	0.455298398937698	17.4462449803813	2.95547513125543e-05	0.000230972405805647	0.425876635308515	19	2.97282658135051	2.80063994622771	3.47025815250396	3.04028067871226	0	0	0	0	5	4	5	5	0	0	0	0
-Nlrp5-ps	-7.13667566529568	1.26371135343783	17.1741869561585	3.41039147548491e-05	0.000263042903888236	0.776139203932954	34	0	0	0	0	3.50079993278464	0.694051630500793	15.2014033935613	1.03850463640395	0	0	0	0	5	1	25	3
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-Mir34b	3.98106265241256	1.74076028897787	17.1127413088565	3.52251976787801e-05	0.00026794633700992	0.42482915888436	54	4.86444908593961	2.0770092728079	17.1653952276879	2.45541277330279	2.23596595965423	0	0	0	8	6	31	6	3	0	0	0
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-Mir680-2	-3.00621463360954	3.15192125250777	16.5842284337432	4.65364140930714e-05	0.000349329266317069	0.344767949944767	134	1.49064397310282	3.56739189762061	2.80063994622771	0.694051630500793	30.4028067871226	5.88485960628905	24.9175092014824	3.68311915995418	2	6	4	1	50	17	45	9
-Wwp1	-3.55687662133219	2.97896138373646	16.4516962689344	4.99055080574729e-05	0.000372171141788082	0.46641320142744	118	0	1.40031997311386	1.38810326100159	2.43222454296981	13.846728485386	2.21488970679844	22.9171858841594	7.4532198655141	0	2	2	4	40	4	56	10
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-Bc1	-1.91746849439176	6.12268036177049	16.3075474507497	5.38490462129734e-05	0.00039439739787455	0.191488237209155	1034	31.010862922865	15.2314013339246	28.7935661883797	18.0063603375538	236.267069736797	31.5119617623154	270.961914797531	59.6884402230682	51	44	52	44	317	53	387	86
-Mir324	2.12107018088344	4.05123077890927	16.3049513757873	5.39228694727693e-05	0.00039439739787455	0.202815721418512	248	14.5390649096553	16.6116728009883	40.1050752972789	23.8503035696451	5.94565316270102	3.50079993278464	11.1048260880127	9.12084203613678	42	30	98	32	10	5	16	15
-Mir741	-4.70184058458898	1.29693630518646	16.1765488644088	5.77040819202755e-05	0.00041869688008688	0.453528863611794	36	0	0	0	0.553722426699609	4.09235462217131	8.19854185206551	2.37826126508041	7.00159986556928	0	0	0	1	10	11	4	10
-Mir291a	-6.53264910162196	0.677054239370747	16.167543842679	5.79790596439325e-05	0.00041869688008688	0.546410140611307	24	0	0	0	0	4.09235462217131	5.96257589241128	2.37826126508041	1.40031997311386	0	0	0	0	10	8	4	2
-2310001H17Rik	-3.8117086915056	1.89505454218894	16.1046423263675	5.99369312860702e-05	0.000430113450298151	0.39935798125311	54	0	0	0	1.03850463640395	7.19839154709492	3.68311915995418	10.4345078117197	8.91847974405152	0	0	0	3	13	9	14	15
-Mir1950	-3.95748808531102	2.38090306875839	15.7243187684919	7.32760035591679e-05	0.000522549500381316	0.529076927011113	78	0	1.2161122714849	0.34616821213465	0.553722426699609	11.4585929420797	2.98128794620564	23.188047334534	2.10047995967078	0	2	1	1	28	4	39	3
-Snord66	-1.27269230808907	8.18728534781423	15.7000629321384	7.4221700724329e-05	0.000522795256794169	0.0937639659318237	4212	185.311785343712	170.863774143629	117.697192125781	135.108272114705	361.764148599944	516.508136680127	479.814210229972	487.311350643622	267	281	340	244	884	693	807	696
-Mir96	-6.51269164739356	0.660234571881598	15.699931807966	7.42268462757716e-05	0.000522795256794169	0.576440925518918	24	0	0	0	0	4.09235462217131	4.47193191930846	0.594565316270102	4.9011199058985	0	0	0	0	10	6	1	7
-BC024386	-6.99602144224204	1.13952184561295	15.5582504393919	8.00017596466698e-05	0.000560012317526689	0.862187047866339	35	0	0	0	0	14.0031997311386	0.694051630500793	8.51278590039432	0	0	0	0	0	20	1	14	0
-5033403H07Rik	-6.44831513297383	0.595627882888442	15.1919689948362	9.71155653815037e-05	0.000675663781099364	0.585378937521072	23	0	0	0	0	6.54021847897112	4.20095991934157	3.47025815250396	0.608056135742452	0	0	0	0	11	6	5	1
-Mir126	1.24352014406418	14.8789235815257	15.17606539914	9.79369487742185e-05	0.000677248839705353	0.0950008604949591	420720	42664.8668205049	20530.1981570697	49061.4681728655	26826.6122547196	35304.4118589672	19508.2825921383	12422.238481493	27186.0023667161	70166	59307	88603	65553	47368	32811	17742	39170
-4930581F22Rik	-4.68347345931895	1.14471528622407	15.1631972873823	9.86066708918126e-05	0.000677772358358784	0.498289202269496	33	0	0	0.553722426699609	0	7.4532198655141	1.7836959488103	9.10207982524007	4.16430978300476	0	0	1	0	10	3	13	6
-Sra1	-6.19692808063838	0.34591044328885	15.1139909313937	0.000101210407797144	0.00069012959141025	0.440765986063492	19	0	0	0	0	3.87605698689727	0.818470924434263	2.98128794620564	3.56739189762061	0	0	0	0	7	2	4	6
-Snord85	-1.347700293414	9.98784551803355	15.1064747121305	0.00010161417296838	0.00069012959141025	0.110905289356566	15092	372.813506079807	549.302304088389	845.471879736084	617.541108143211	2640.17240242502	1852.74704560725	392.208584348558	1747.54797866397	911	737	1422	882	3804	3047	1133	3156
-Gm16023	-4.84906479740497	2.04843453239765	14.9318719681594	0.000111463899395583	0.000752261048033047	0.781248660083243	61	0	0	1.10744485339922	0	11.1798297982712	0	28.7065594488341	2.08215489150238	0	0	2	0	15	0	41	3
-Mir1960	3.96705781998388	1.29508911386833	14.9214563693412	0.000112080962458911	0.000752261048033047	0.41501288861623	36	2.0770092728079	3.87605698689727	6.13853193325697	4.47193191930846	0	0	0.694051630500793	0.608056135742452	6	7	15	6	0	0	1	1
-0610008F07Rik	-4.54488558953107	1.15637169454961	14.5761546583671	0.000134607153569803	0.000898168200135353	0.478560111450913	34	0	0	0	0.74532198655141	9.51304506032163	5.60127989245543	3.47025815250396	2.43222454296981	0	0	0	1	16	8	5	4
-Mir30c-1	1.27691626836962	5.65565459422496	14.2837634742279	0.000157215137919935	0.00104292135096887	0.0942811372414155	732	60.0510969432802	62.3142388035666	139.504377730659	69.926455610382	27.3472887586373	28.2398437616801	14.3232411775996	45.464641179636	101	89	201	115	79	51	35	61
-Mir674	1.68665633785934	4.7344282331729	14.2584368876227	0.000159344901134507	0.0010509394924536	0.157762238651678	392	41.025006822637	30.8070394085048	91.6148152261047	31.6189190586075	8.65420530336624	12.1818933873914	4.50159008438844	27.5769135024022	69	44	132	52	25	22	11	37
-Mir328	1.21754727845112	7.37025735114261	14.1902387757875	0.000165225411008837	0.00108346088483381	0.0938897453017011	2362	163.284949424635	204.218224315086	326.416358632286	256.258555079836	210.991695672241	91.8164764971102	43.2710265168312	107.422150779724	399	274	549	366	304	151	125	194
-Mir320	1.26517933587612	6.72859295410854	14.1369883832178	0.000169968606945481	0.00110819531728454	0.099920171450282	1651	126.317396751144	100.329262397505	222.58616040258	99.6700368059297	74.4808541235179	79.0041305744495	47.5652253016081	79.1180784809329	182	165	643	180	182	106	80	113
-0610012G03Rik	-6.06136339421713	0.203387180072876	14.0001848254456	0.00018279266393932	0.00118503653156116	0.456186711370962	17	0	0	0	0	4.16430978300476	2.43222454296981	1.73084106067325	1.10744485339922	0	0	0	0	6	4	5	2
-Snhg1	-1.13576202936067	11.3097299616808	13.97049833596	0.000185701763943309	0.00119709442180404	0.0862756069742781	37837	1580.35556265031	1148.61804041749	1763.72704082604	1264.14830015521	3349.59225824722	4315.41430213266	3851.59411879772	4088.93432149246	2277	1889	5095	2283	8185	5790	6478	5840
-Mir433	6.22949339947389	0.286675210706276	13.9241156368209	0.000190340641944053	0.00122010490145036	0.635106526064817	17	0.694051630500793	1.2161122714849	1.73084106067325	4.98350184029649	0	0	0	0	1	2	5	9	0	0	0	0
-6430411K18Rik	6.22955452291459	0.286828886351783	13.9015924293055	0.000192635189076567	0.00122791480858303	0.63776153052932	17	0.608056135742452	0.6923364242693	2.76861213349805	3.68311915995418	0	0	0	0	1	2	5	9	0	0	0	0
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-Snord68	-1.13457444274774	8.92132519667897	12.7118658261147	0.000363342726950629	0.0020046158463653	0.0936159992954593	7303	159.237377581939	195.464016624962	433.789589950159	280.24106694333	977.465379948047	906.707182591222	558.711562553138	796.553537822612	460	353	1060	376	1644	1295	805	1310
-Slc25a44	-2.96909247201373	2.37553272872162	12.7112171467032	0.00036346878335363	0.0020046158463653	0.406906467452325	77	0.818470924434263	0.74532198655141	1.7836959488103	1.40031997311386	15.2691358710174	1.82416840722736	11.4235510004434	6.0909466936957	2	1	3	2	22	3	33	11
-Mir186	1.18971925817329	10.3333935373353	12.7014824275027	0.000365365815963977	0.0020046158463653	0.103706182462682	18235	2194.9732503939	1436.46980410857	2902.16314427847	1881.57397028765	1238.61034850737	496.405216201088	408.647150904312	740.306951150791	2945	2416	4145	2711	2037	1434	738	1809
-Bmp1	-3.97471936953623	1.38701445027206	12.7011339267468	0.000365433914148977	0.0020046158463653	0.543071332932969	39	0	0.700159986556928	0.694051630500793	0	4.50018675775045	1.66116728009883	7.36623831990836	2.23596595965423	0	1	1	0	13	3	18	3
-Pglyrp2	-6.68358905274349	0.818938124586529	12.6644090443586	0.00037268230723405	0.00203459575384713	1.04491512795468	27	0	0	0	0	4.91082554660558	0	8.91847974405152	0	0	0	0	0	12	0	15	0
-U05342	-3.57180440937422	1.81969552214636	12.6294872731998	0.000379709308836468	0.00206308724467814	0.533167133824104	54	0	0.608056135742452	1.03850463640395	0	8.18470924434263	2.23596595965423	14.2695675904824	2.10047995967078	0	1	3	0	20	3	24	3
-Mir34a	1.91945112130955	3.61902087448453	12.6166339601411	0.000382329185895629	0.00206747678249722	0.209108419099582	180	10.2308865554283	20.1236936368881	36.2684842924762	19.604479623594	8.32861956600951	3.64833681445471	3.4616821213465	6.0909466936957	25	27	61	28	12	6	10	11
-Mtfr1	-4.04881533517461	1.45196702496999	12.5820304874237	0.000389473361755969	0.0020961750271866	0.587826977228111	40	0	0.34616821213465	0.553722426699609	0	7.4532198655141	1.1891306325402	15.4035197042524	2.77620652200317	0	1	1	0	10	2	22	4
-Snord49b	-1.26067966372732	6.59754559587082	12.5629346353204	0.000393473367643403	0.00210776109146067	0.111486118172609	1485	36.8630496087463	39.9091192337449	149.915152188171	57.7653328955329	136.044107368917	135.661994541404	50.3359618527072	219.124664046115	62	57	216	95	393	245	123	294
-Ank1	1.35227733675525	11.2588220131714	12.4614990275367	0.000415426418612258	0.00221496048428311	0.135867548702657	33776	2895.96829163896	2268.80140253178	5907.42206540648	3041.79615803784	1106.25277875995	862.012125081985	2438.30510432723	1082.81416755718	5230	5544	7926	5116	1580	1242	4010	3128
-4833418N02Rik	-2.07313530572046	3.53931042163891	12.4439824566212	0.000419340681838063	0.00222543124640572	0.244921651041945	170	6.70789787896269	1.7836959488103	9.802239811797	4.16430978300476	20.6739086152434	9.69270993977019	28.2398437616801	10.2308865554283	9	3	14	6	34	28	51	25
-Mir340	-1.24781368093967	8.59679560345445	12.360285434567	0.000438563635265595	0.0023166717955465	0.11588698056633	5906	175.120167093826	82.3880344880466	585.838327448187	100.671923705414	896.622349821346	438.789203407335	966.220781448561	524.008981028099	288	238	1058	246	1203	738	1380	755
-Pknox1	-5.96867464377884	0.108276776805556	12.3202806513909	0.00044806332818544	0.00235594588691054	0.585510339236401	16	0	0	0	0	3.32233456019766	0.818470924434263	5.21725390585987	0.594565316270102	0	0	0	0	6	2	7	1
-Mir3107	1.3508075738813	10.2573409434783	12.2375775967787	0.000468365962224657	0.00245140166467126	0.137805722557386	16873	1553.00460609751	1938.04284278958	2747.75040515264	1553.58342682196	273.126719374239	343.861626980457	820.517101745348	1165.68358696641	2612	2768	3959	2555	789	621	2005	1564
-Mir486	1.35080726179605	10.2573415082787	12.2166008121444	0.000473661512742678	0.00246779810976893	0.13804319607134	16873	1828.8178848867	1921.13491322619	2407.29424140437	884.45978200403	436.886994665992	254.135222036839	1494.37058303558	929.900154646439	2612	2768	3959	2555	789	621	2005	1564
-Gm15787	-5.84922159415344	-0.0267336728102733	12.0781096044983	0.000510173001972336	0.0026459427056838	0.520917363420797	14	0	0	0	0	1.10744485339922	2.45541277330279	1.49064397310282	2.37826126508041	0	0	0	0	2	6	2	4
-Snord23	-3.10776202871609	2.42787154463463	12.0107649436004	0.000528941434547806	0.00273086957836673	0.509625657247902	83	1.10744485339922	0	5.21725390585987	0	19.604479623594	2.77620652200317	21.8900208867283	2.0770092728079	2	0	7	0	28	4	36	6
-Snord1a	-1.79805603420245	3.92918303968764	11.9925876763572	0.000534125716115637	0.00274521370309884	0.200145509933857	230	4.9011199058985	6.24646467450714	16.4175156650462	2.7693456970772	34.3307904553758	22.0987149597251	23.8503035696451	18.4315248043731	7	9	27	8	62	54	32	31
-Snord42b	-1.18512884296518	6.24789852349338	11.9040618509162	0.000560116711777104	0.00285518663749724	0.101627779377629	1095	48.5836141350555	40.1317049590018	30.4628026678492	45.9589614160676	92.8964499232888	170.678734920273	81.4554483290039	136.531197378601	70	66	88	83	227	229	137	195
-Snhg7	-2.34268751527016	3.5610429386213	11.9026964396979	0.000560527438036267	0.00285518663749724	0.338566530531322	173	2.21488970679844	1.22770638665139	11.1798297982712	4.16195721389071	23.8054395429356	10.4107744575119	49.860603130881	4.50018675775045	4	3	15	7	34	15	82	13
-1700001L05Rik	-5.950973384031	0.0930486569679726	11.7459555862755	0.000609755940371602	0.00309214012428443	0.654968245797187	16	0	0	0	0	4.47193191930846	0	4.20095991934157	2.77620652200317	0	0	0	0	6	0	6	4
-Rnf44	-3.56352892254898	2.54220698820135	11.7368125443015	0.000612758782003269	0.00309361845250323	0.670391576244117	88	0.818470924434263	1.49064397310282	1.1891306325402	0	22.2096521760254	0	15.9237377581939	2.21488970679844	2	2	2	0	32	0	46	4
-Trmt61b	-6.04462877508772	0.197297525490101	11.686250899599	0.000629636409648177	0.00316482442030207	0.741746117911198	18	0	0	0	0	6.68861749316697	0.6923364242693	2.76861213349805	0	0	0	0	0	11	2	5	0
-Def8	-5.9906404918121	0.123717443385779	11.628655678048	0.000649434749337637	0.0032500221447116	0.700504873096256	16	0	0	0	0	1.73084106067325	0.553722426699609	3.68311915995418	0.74532198655141	0	0	0	0	5	1	9	1
-Mir878	-5.70475205457436	-0.1626146032132	11.6151126935116	0.000654180742215014	0.00325947697321978	0.47390488168473	13	0	0	0	0	1.22770638665139	0.74532198655141	2.97282658135051	2.80063994622771	0	0	0	0	3	1	5	4
-Mir511	-1.91950371805125	3.59489884941376	11.5870640997842	0.000664121779537945	0.0032946215237078	0.22775643116366	183	4.9011199058985	6.24646467450714	9.72889817187923	1.3846728485386	31.5621783218777	14.3232411775996	14.1611177444768	21.4043513857237	7	9	16	4	57	35	19	36
-AI506816	-5.56956186604363	-0.292465011885234	11.5304780492608	0.000684644063235273	0.00338172673658635	0.377489090786083	12	0	0	0	0	2.21488970679844	0.818470924434263	2.98128794620564	1.1891306325402	0	0	0	0	4	2	4	2
-Mir335	1.11656851457955	6.55078457560659	11.3673264027419	0.000747473949853804	0.00367615421027237	0.0963844774767941	1318	137.884567512011	120.696759202831	200.245756155281	135.340067947655	83.9117467324583	34.9629894255996	39.8680147223719	56.4744937859641	185	203	286	195	138	101	72	138
-Mir210	1.3815129543114	5.22746528492104	11.3305689566611	0.000762415382904168	0.00373354485791268	0.14042671192209	592	60.3710809106642	26.7554392321546	170.83903671989	40.9490461995468	42.5639295019716	6.92336424269299	20.4877297878855	14.7324766398167	81	45	244	59	70	20	37	36
-4931408D14Rik	-6.38756698788491	0.523260717236992	11.280671896319	0.00078318206252862	0.00381884928779981	1.07304045821678	22	0	0	0	0	5.53722426699609	0	8.94386383861692	0	0	0	0	0	10	0	12	0
-1810026B05Rik	-5.8169788152171	-0.032347099625177	11.2635797850259	0.00079042631245266	0.0038377720106744	0.626059377853638	15	0	0	0	0	2.7693456970772	0.553722426699609	2.04617731108566	0.74532198655141	0	0	0	0	8	1	5	1
-Mir190	1.91702509695609	3.42954120734986	11.2262346008614	0.0008064910540028	0.00388883762828111	0.233988281959687	163	8.18470924434263	14.1611177444768	38.6467455575566	17.5039996639232	6.94051630500793	5.47250522168207	1.73084106067325	5.53722426699609	20	19	65	25	10	9	5	10
-1810058I24Rik	-3.42873979152306	1.78663120652355	11.2233161109447	0.000807760313674517	0.00388883762828111	0.562407933094681	50	0	1.1891306325402	1.40031997311386	0	6.08056135742452	0.6923364242693	15.5042279475891	2.45541277330279	0	2	2	0	10	2	28	6
-Meg3	5.71546848310332	-0.241674554922147	11.1958611597532	0.000819799822226995	0.00393021679479412	0.613085247102082	12	2.43222454296981	1.3846728485386	2.21488970679844	0	0	0	0	0	4	4	4	0	0	0	0	0
-2410004N09Rik	-4.48657037659986	1.6757068910884	11.0955922012835	0.000865331464948072	0.00413114310253452	0.959371087373287	50	0	0	0.818470924434263	0	13.0804369579422	0	18.0453423930206	0	0	0	2	0	22	0	26	0
-Snord65	1.99835877269016	4.70192846623195	11.0805491937091	0.000872379596812486	0.00414743799984603	0.295394767173396	320	40.9754595757711	36.8311915995418	5.96257589241128	40.4304415063669	20.3046396101509	11.7988777185135	11.5530665791066	5.19252318201975	74	90	8	68	29	17	19	15
-Tysnd1	-5.73739359459806	-0.138947738722222	11.049738354647	0.000886997153791899	0.00419943465757907	0.58228515939149	13	0	0	0	0	1.40031997311386	0.694051630500793	4.25639295019716	1.03850463640395	0	0	0	0	2	1	7	3
-Mirlet7i	1.07302198102237	10.7310252728864	11.0393926184035	0.000891960799917054	0.00420548459795603	0.0976465050666323	26242	1668.36567164592	985.438993018852	7299.68353628451	1646.35136075191	1767.90396605624	1045.9358071647	1359.00546338438	689.220910360088	3013	2408	9794	2769	2525	1507	2235	1991
-Mir3098	-1.79653680485735	4.13275156820863	10.9996036948799	0.000911313713823056	0.00427904916655188	0.225289324612017	259	8.40191983868314	10.4107744575119	12.161122714849	2.42317748494255	36.5456801621742	8.18470924434263	62.6070468703184	20.8097860694536	12	15	20	7	66	20	84	35
-Zfp862	-6.00900695330373	0.137260173296749	10.9587797077338	0.000931611478588379	0.00435642908634976	0.827218325136608	16	0	0	0	0	2.21488970679844	0	7.4532198655141	1.1891306325402	0	0	0	0	4	0	10	2
-Gm8883	-6.00903518142652	0.137235780049281	10.9392834847835	0.000941465710262349	0.00438203576977106	0.830808243916824	16	0	0	0	0	2.37826126508041	0	6.94051630500793	1.2161122714849	0	0	0	0	4	0	10	2
-Mir136	1.48579773526204	5.56288024723084	10.9261992834096	0.000948138063898294	0.00438203576977106	0.174066319140284	753	59.6257589241128	45.1869640365277	210.047995967078	61.7705951145706	80.2634099180036	12.4620556368474	7.19839154709492	11.0493574798625	80	76	300	89	132	36	13	27
-Mir3071	1.4857985362653	5.5628798270356	10.9252793760163	0.000948608970318538	0.00438203576977106	0.174082205996986	753	55.5241304400634	46.2122663164263	103.850463640395	49.2812959762652	54.0190810126613	26.8315915158508	7.72934911151132	18.9043196370371	80	76	300	89	132	36	13	27
-Snora17	-2.46127401857233	3.40420342285319	10.874005626142	0.00097523375467	0.00448686175031641	0.40851922722979	155	2.10047995967078	2.08215489150238	7.29667362890942	2.0770092728079	17.7191176543875	3.68311915995418	61.1164028972156	4.75652253016081	3	3	12	6	32	9	82	8
-Clip4	5.52952392001519	-0.458726906169357	10.7824070833312	0.00102469341988096	0.00469548269913325	0.502799642510046	10	0.409235462217131	2.98128794620564	1.1891306325402	2.10047995967078	0	0	0	0	1	4	2	3	0	0	0	0
-Tor2a	-6.05348342746507	0.174493511900422	10.7693806553913	0.00103193034471589	0.00470973009328334	0.896944340718012	16	0	0	0	0	1.40031997311386	0	6.68861749316697	1.03850463640395	0	0	0	0	2	0	11	3
-Mir128-2	3.80595315755454	1.17261315395944	10.7419570699145	0.00104733513871024	0.00476099359867881	0.634080706784321	35	3.47025815250396	0	6.2310278184237	5.53722426699609	0	0.74532198655141	0	0.700159986556928	5	0	18	10	0	1	0	1
-Hspa13	-5.59458897523584	-0.27627009189198	10.6867872417783	0.0010790343663428	0.00488562782538546	0.521237684268079	12	0	0	0	0	1.66116728009883	0.409235462217131	4.47193191930846	1.1891306325402	0	0	0	0	3	1	6	2
-D830015G02Rik	4.14283168053781	0.551973657077271	10.6760953370882	0.00108528904983538	0.00489452492435639	0.576712851276144	19	2.08215489150238	3.04028067871226	0.6923364242693	4.42977941359688	0	0	0	0.700159986556928	3	5	2	8	0	0	0	1
-Tmem41a	-5.72440095395471	-0.127430607973083	10.5566366819088	0.00115771656627495	0.00520060866976266	0.666956066151007	14	0	0	0	0	2.42317748494255	0	2.04617731108566	1.49064397310282	0	0	0	0	7	0	5	2
-Snhg8	-1.83987674889479	3.46416913391953	10.5096082183788	0.0011875543104793	0.00531372340492893	0.228182931549006	164	4.85836141350555	3.04028067871226	4.8463549698851	4.42977941359688	17.1878894131195	26.8315915158508	11.2967410091319	23.1052795563786	7	5	14	8	42	36	19	33
-1810064F22Rik	-5.71185796121916	-0.138019637864516	10.4694796589287	0.00121362897199574	0.00540313207893838	0.672791990598712	14	0	0	0	0	4.42977941359688	0.818470924434263	2.98128794620564	0	0	0	0	0	8	2	4	0
-A530013C23Rik	-5.70467836394175	-0.143280603126766	10.4643449167901	0.00121700696256544	0.00540313207893838	0.668292869459531	14	0	0	0	0	3.27388369773705	2.98128794620564	0	1.40031997311386	0	0	0	0	8	4	0	2
-4732471J01Rik	-2.40361917198915	2.3838183502368	10.4213715563006	0.00124565349249119	0.00550887842997075	0.332913698975582	78	2.21488970679844	0	2.23596595965423	2.37826126508041	17.5039996639232	6.94051630500793	8.51278590039432	6.2310278184237	4	0	3	4	25	10	14	18
-D830005E20Rik	5.29021647337736	-0.682320418680887	10.3493783559945	0.00129518294778252	0.00570580595915001	0.358026721476975	9	1.66116728009883	0.818470924434263	2.23596595965423	0.594565316270102	0	0	0	0	3	2	3	1	0	0	0	0
-Atp2a2	2.0123235287421	4.868592175877	10.3240172903538	0.00131310157750702	0.00576249576898274	0.326890138977092	394	51.8118390052127	58.3003369620666	47.4283785879112	23.5394384251562	21.0414522145852	0.818470924434263	35.7754553544677	1.1891306325402	74	84	78	68	38	2	48	2
-Lrrc28	-3.51474895709429	2.08366925878611	10.2057873690644	0.0014000060627547	0.00611767150380119	0.701657354307468	60	0	1.49064397310282	0	1.40031997311386	8.32861956600951	1.2161122714849	13.846728485386	1.10744485339922	0	2	0	2	12	2	40	2
-AV039307	-6.20159006204567	0.324020684262981	10.1995373444327	0.00140475892550036	0.00611767150380119	1.14514068085484	18	0	0	0	0	2.77620652200317	0	4.8463549698851	0	0	0	0	0	4	0	14	0
-Snord19	-1.0382015661787	7.22385150526551	10.1767515297517	0.00142222528934907	0.00616001156039107	0.0955181999794412	2203	51.2328953959282	65.3392463505539	136.275408918305	90.1839603727206	217.610905754857	219.850235778875	322.734008182869	205.522973880949	148	118	333	121	366	314	465	338
-Snord34	-2.08475017146841	2.83962853955605	10.1727972396382	0.00142527874841651	0.00616001156039107	0.285645529074013	110	1.3846728485386	1.66116728009883	5.32006100882271	0.74532198655141	20.2152207531835	14.7033597176955	10.4107744575119	11.5530665791066	4	3	13	1	34	21	15	19
-Gm10319	-5.60183019030439	-0.272283085597053	10.1165026412179	0.00146947577925262	0.00632706363821601	0.628336599585883	12	0	0	0	0	1.22770638665139	0.74532198655141	4.16195721389071	0.700159986556928	0	0	0	0	3	1	7	1
-Mir551b	-5.28945446764904	-0.570019864619093	9.96896126389673	0.00159201283526663	0.00682889716180158	0.368842494562338	10	0	0	0	0	1.63694184886853	1.49064397310282	0.594565316270102	2.10047995967078	0	0	0	0	4	2	1	3
-2700038G22Rik	1.0991587512314	5.82706341644059	9.95941636790478	0.00160028777214299	0.0068386829513676	0.103563390951204	872	64.213054157171	70.0159986556928	223.484625021255	41.3478172304867	31.1551390921185	32.1159007485773	27.8280114307649	43.2286752199818	108	100	322	68	90	58	68	58
-Snora24	-1.78976990973169	3.42523406404003	9.931884623743	0.00162440130550695	0.00691582794620685	0.228501461205898	160	3.87605698689727	2.04617731108566	10.4345078117197	4.75652253016081	29.406719435391	22.9037038065262	11.5530665791066	11.0773827883088	7	5	14	8	42	33	19	32
-Wac	-3.6951273770279	1.25653637775457	9.84734492230561	0.00170077053129811	0.00721404898219758	0.650342173610494	36	0	0	0	1.10744485339922	6.13853193325697	1.49064397310282	8.91847974405152	1.40031997311386	0	0	0	2	15	2	15	2
-Mirlet7d	1.01253633956975	10.1217350046956	9.79739851990192	0.00174758920538644	0.00738518253091085	0.0980317463946137	16847	721.068385876475	955.171186056826	2209.87149597251	1445.92465390974	1258.6947745438	920.710382322361	553.159149509132	893.842519541404	2083	1725	5400	1940	2117	1315	797	1470
-Mir3057	1.56624574489393	4.13735216248517	9.71249631557864	0.00183019242429111	0.00770571791924781	0.195683754696777	244	25.6799103285293	25.538357701183	18.6930834552711	24.3637867747828	8.59394470655976	18.6330496637853	5.35108784643091	8.40191983868314	37	42	54	44	21	25	9	12
-4930483K19Rik	-4.07599496401445	0.707807703877924	9.68729747922232	0.00185546239279753	0.00778339187566907	0.650201622154782	24	0	0	0	0.608056135742452	2.7693456970772	1.66116728009883	4.50159008438844	0.74532198655141	0	0	0	1	8	3	11	1
-Abhd1	-5.66647646801464	-0.198980726318646	9.61449776551205	0.00193047250374198	0.00806838507974211	0.798215818999853	13	0	0	0	0	2.04617731108566	0	4.16195721389071	0.700159986556928	0	0	0	0	5	0	7	1
-4931403E22Rik	-5.96978485173564	0.0998305059838412	9.60001485906455	0.00194575794845059	0.00810259058095667	1.08621383004923	16	0	0	0	0	3.64833681445471	0	5.53722426699609	0	0	0	0	0	6	0	10	0
-Tmem179b	-5.91733615380083	0.0555854404990001	9.5767299128365	0.00197059084015365	0.00817616054041931	1.04701992451759	16	0	0	0	0	5.55241304400634	0	2.7693456970772	0	0	0	0	0	8	0	8	0
-Gm16551	-5.39818426417959	-0.456472505628428	9.54681648699309	0.0020029650635253	0.00828037368653032	0.557166179690809	11	0	0	0	0	2.76861213349805	0	2.23596595965423	1.7836959488103	0	0	0	0	5	0	3	3
-Mir467c	-3.19133751128218	1.23147666370608	9.50360214880608	0.00205068921842834	0.00842076289090342	0.504945662631203	35	0.608056135742452	0	0.553722426699609	0.409235462217131	8.94386383861692	1.7836959488103	9.802239811797	2.08215489150238	1	0	1	1	12	3	14	3
-Mir379	1.8411314595372	3.36114899756091	9.50271175811926	0.00205168456062327	0.00842076289090342	0.262009063995429	153	14.5933472578188	7.96186887909694	28.2398437616801	7.77547378212549	14.9064397310282	4.16195721389071	3.50079993278464	2.77620652200317	24	23	51	19	20	7	5	4
-4933405D12Rik	-4.20339477654173	0.833797599470417	9.48229754646459	0.00207463988425776	0.00848445916823692	0.76728472152477	26	0	0	0	0.34616821213465	4.42977941359688	1.63694184886853	9.68918582516833	0	0	0	0	1	8	4	13	0
-Mir205	-5.5496472784481	-0.289774410021733	9.45142550093119	0.00210985060915748	0.00859764123231674	0.735049022988572	13	0	0	0	0	5.35108784643091	1.40031997311386	0	1.2161122714849	0	0	0	0	9	2	0	2
-Mir1a-2	3.96385634049465	0.456332250134469	9.4183755919052	0.00214821737610278	0.00872283283321451	0.633681733191561	23	0.6923364242693	0.553722426699609	6.5477673954741	2.23596595965423	0	0	0	0.608056135742452	2	1	16	3	0	0	0	1
-Mir1b	3.96366007425221	0.456164631557195	9.40381428072631	0.00216534504927928	0.00876120106818318	0.635507314511787	23	1.40031997311386	0.694051630500793	9.72889817187923	1.03850463640395	0	0	0	0.594565316270102	2	1	16	3	0	0	0	1
-Rnu12	-2.0789573310526	3.77260980645493	9.37294121968574	0.00220211893578888	0.00887850779411699	0.355055174324306	212	4.75652253016081	5.60127989245543	7.63456793550872	4.86444908593961	32.1936437285224	2.76861213349805	27.0095405063307	9.68918582516833	8	8	11	8	93	5	66	13
-Cldn25	-5.62670660260646	-0.254133994120215	9.26347528762952	0.00233769010488806	0.00937375843488922	0.833753133549746	12	0	0	0	0	1.10744485339922	0	5.96257589241128	1.1891306325402	0	0	0	0	2	0	8	2
-Snord69	-0.990680806137596	7.25666151567352	9.2605822201903	0.00234138576156304	0.00937375843488922	0.0959745173213836	2301	109.925117889438	72.8754212025833	243.830510432723	40.501680819754	243.637867747828	139.549292616042	303.346048526424	197.990250317944	157	105	401	117	440	341	407	333
-Schip1	3.99609034629807	0.424115359917217	9.23151685898449	0.00237884494599487	0.00949042686496556	0.652017730969643	17	3.32233456019766	2.45541277330279	0.74532198655141	1.7836959488103	0	0	0.608056135742452	0	6	6	1	3	0	0	1	0
-C330022C24Rik	-5.86791058522248	-0.00112585493013314	9.22013376430013	0.00239368057698804	0.00951633985485487	1.08856934734907	15	0	0	0	0	3.64833681445471	0	4.98350184029649	0	0	0	0	0	6	0	9	0
-2700089E24Rik	-3.31825238706569	2.2242433349291	9.19606448069847	0.00242536006842217	0.00960880499329756	0.74313806927634	70	0.694051630500793	0.608056135742452	0	1.66116728009883	11.0493574798625	0	21.4043513857237	1.40031997311386	1	1	0	3	27	0	36	2
-Mirlet7b	0.937138218982313	9.38818883152705	9.17750884023032	0.00245007280130308	0.0096731247968402	0.0895107516917409	10012	743.649219057575	420.694055159211	2223.29548588286	671.264242068945	893.40414284664	545.524581573623	398.276768911306	281.088588253336	1343	1028	2983	1129	1276	786	655	812
-Dmr	-5.77170314815234	-0.0797406660206753	9.13087854946811	0.00251330999291549	0.00988857483419507	1.02707333968874	15	0	0	0	0	4.42977941359688	0	0	4.16195721389071	0	0	0	0	8	0	0	7
-Mir668	3.65464394045293	0.0447295147058579	9.04222855064229	0.00263813851840573	0.0103440414072197	0.420750050074846	15	2.77620652200317	1.2161122714849	1.73084106067325	1.66116728009883	0.409235462217131	0	0	0	4	2	5	3	1	0	0	0
-AW112010	-3.81468417960031	1.20869686190852	9.02944763887385	0.0026566474478555	0.0103809408835724	0.81558416289978	34	0.594565316270102	0	0.694051630500793	0	3.11551390921185	0	8.59394470655976	1.49064397310282	1	0	1	0	9	0	21	2
-Rnu11	-1.99169858610028	4.26616621222318	9.00298526824096	0.00269538963278575	0.0104963807884251	0.357732874849185	297	4.86444908593961	4.1540185456158	16.6116728009883	3.27388369773705	77.5134866013466	6.54021847897112	81.2185584406037	5.55241304400634	8	12	30	8	104	11	116	8
-4933406I18Rik	-5.51419893511843	-0.369915742190644	8.99409538905896	0.00270853316627777	0.0105116882405542	0.784549158060522	11	0	0	0	0	0.694051630500793	0	2.0770092728079	2.21488970679844	0	0	0	0	1	0	6	4
-Nagpa	-3.26321422407828	0.711913571681929	8.9343928467794	0.00279850477796738	0.0108240472937653	0.461375279778792	24	0.74532198655141	0	0.700159986556928	0	3.64833681445471	1.73084106067325	3.87605698689727	1.63694184886853	1	0	1	0	6	5	7	4
-Ncaph2	-3.24794657364615	1.40236514138266	8.87893430752886	0.00288479887931402	0.0111201200043827	0.608383042258691	39	0.34616821213465	0	0	1.49064397310282	8.32391442778142	3.50079993278464	11.1048260880127	0.608056135742452	1	0	0	2	14	5	16	1
-Snord35a	-1.86645078488422	3.1958895587416	8.80397854951295	0.00300574374395181	0.0115130374700931	0.277855654184593	131	5.60127989245543	4.16430978300476	4.25639295019716	1.73084106067325	13.8430606674902	9.41241563099402	29.067557475505	10.7021756928618	8	6	7	5	25	23	39	18
-Hdac10	-6.29766277932921	0.409438374965166	8.80327031569925	0.00300691075029599	0.0115130374700931	1.62403963994052	18	0	0	0	0	0	0	10.7021756928618	0	0	0	0	0	0	0	18	0
-B830017H08Rik	5.32941621896309	-0.686862415819199	8.71729469417869	0.0031520542327124	0.0120284076238289	0.721384416134407	8	1.22770638665139	2.23596595965423	0	1.40031997311386	0	0	0	0	3	3	0	2	0	0	0	0
-Mir483	4.95299475147863	-1.03855334834364	8.66099771495384	0.00325093246385866	0.0123371020106544	0.31761008964285	7	0.694051630500793	1.2161122714849	0.6923364242693	1.10744485339922	0	0	0	0	1	2	2	2	0	0	0	0
-Mir221	0.922265525125667	8.55842785260915	8.65895835066664	0.00325457292305608	0.0123371020106544	0.0912934836443556	5659	255.125972343237	338.878125140161	689.970989298083	450.174479877052	464.355512006949	267.461114864747	257.493154915794	295.515281970832	737	612	1686	604	781	382	371	486
-Hyi	-5.37191465404839	-0.513083591072126	8.54364069953964	0.00346731428867763	0.0131000185542423	0.750122172843921	10	0	0	0	0	0.694051630500793	0	1.73084106067325	2.21488970679844	0	0	0	0	1	0	5	4
-AF357399	-2.02509274782888	2.62961192791143	8.52849192173923	0.00349629285179349	0.0131459115540079	0.310477511331951	89	2.21488970679844	1.22770638665139	2.98128794620564	2.97282658135051	12.6028797580247	8.32861956600951	15.8094595293037	5.88485960628905	4	3	4	5	18	12	26	17
-Mir218-1	4.89509483633198	-1.07472502168	8.52526158730094	0.00350250404243506	0.0131459115540079	0.294529197532838	7	0.553722426699609	0.409235462217131	2.23596595965423	1.1891306325402	0	0	0	0	1	1	3	2	0	0	0	0
-Crem	-3.57926858214912	0.093385262246104	8.44067526067868	0.00366919976852365	0.0137264161832311	0.43650542752889	16	0	0	0.409235462217131	0	2.97282658135051	1.40031997311386	2.08215489150238	3.04028067871226	0	0	1	0	5	2	3	5
-Cacnb2	4.95159972901503	-1.03756393439504	8.4103747432516	0.00373085748437516	0.0139114653257257	0.377642228096051	7	2.08215489150238	0.608056135742452	0.6923364242693	0.553722426699609	0	0	0	0	3	1	2	1	0	0	0	0
-Numb	-2.15585722667369	2.43904569134592	8.3909714925846	0.00377089311820349	0.0140149480386651	0.357897850116302	80	2.80063994622771	1.38810326100159	3.64833681445471	0.6923364242693	11.0744485339922	3.27388369773705	22.3596595965423	4.75652253016081	4	2	6	2	20	8	30	8
-Snora64	-2.80236496230048	1.59221260392222	8.35365855518681	0.00384911525753426	0.0142592224313201	0.554109016621612	47	0	0	2.76861213349805	0.409235462217131	13.4157957579254	4.16195721389071	10.5023997983539	0.694051630500793	0	0	5	1	18	7	15	1
-Mir92-2	-0.974195409614297	7.79620997802811	8.27349220919526	0.00402280557443	0.0148399286867159	0.105313036321083	3238	167.215437329174	67.5028013662567	151.719944915693	99.0349818565458	570.91664169838	311.552225725533	214.949115872977	454.603817978019	275	195	274	242	766	524	307	655
-1700012B15Rik	-3.71464754573846	0.363301874486619	8.26940017368961	0.00403188246527775	0.0148399286867159	0.581673238061597	19	0	0	0	0.34616821213465	3.87605698689727	0.818470924434263	5.96257589241128	0.594565316270102	0	0	0	1	7	2	8	1
-Rreb1	-2.28698243842595	2.86069815395797	8.15968905871472	0.00428317140719232	0.0157141433299243	0.46155938291093	113	2.10047995967078	2.77620652200317	5.47250522168207	0.6923364242693	25.471231628182	1.22770638665139	31.3035234351592	2.37826126508041	3	4	9	2	46	3	42	4
-Ccl25	-5.04971900304356	-0.841015363596638	8.12538916599192	0.00436496134325028	0.0159628874764377	0.493136361754168	8	0	0	0	0	0.553722426699609	0.409235462217131	2.98128794620564	1.1891306325402	0	0	0	0	1	1	4	2
-1300002E11Rik	-4.27085129798674	0.913088381500286	8.06223132333958	0.00451974874521871	0.0164761447868835	1.0675323386472	28	0.553722426699609	0	0	0	7.00159986556928	0	10.3369543076217	0	1	0	0	0	10	0	17	0
-Mir450b	1.53561629878188	3.79888996155825	8.02621551756357	0.00461050735129575	0.016753467795632	0.22585969880479	205	23.8054395429356	18.7393940235214	40.7397610947443	7.96186887909694	9.41328125389336	7.77547378212549	2.98128794620564	8.32391442778142	34	27	67	23	17	19	4	14
-Snord42a	1.37473053772198	5.0749280490694	7.96649206637177	0.0047651195395581	0.0172603218877327	0.201409759579643	438	51.4961856830637	40.9235462217131	22.3596595965423	40.4304415063669	42.7097591799726	21.5156005455246	12.161122714849	12.1158874247127	93	100	30	68	61	31	20	35
-Mir704	-4.81767995439293	-1.0639345641914	7.95753441632376	0.00478876043778264	0.0172910622136392	0.265251638190652	7	0	0	0	0	0.6923364242693	0.553722426699609	0.818470924434263	1.49064397310282	0	0	0	0	2	1	2	2
-Gm5105	4.96536868003461	-1.02507804781198	7.94289950623894	0.00482764204552365	0.0173764655329416	0.519901321793637	7	1.82416840722736	0.6923364242693	1.10744485339922	0	0	0	0	0	3	2	2	0	0	0	0	0
-A730017L22Rik	-3.87318424349948	0.518718416663479	7.8967840964419	0.00495227663831838	0.017769017749438	0.772709732011105	21	0.608056135742452	0	0	0	5.21725390585987	1.7836959488103	7.00159986556928	0	1	0	0	0	7	3	10	0
-5730420D15Rik	-5.01564384886024	-0.865600873478205	7.76307010642554	0.00533252424309005	0.019073386085786	0.560350556242892	8	0	0	0	0	0.818470924434263	0	2.37826126508041	1.40031997311386	0	0	0	0	2	0	4	2
-Snora7a	-2.26792863685883	2.37127807649404	7.75582983890058	0.00535394359705501	0.0190901551382493	0.444782255282773	80	0.608056135742452	1.3846728485386	3.87605698689727	0.409235462217131	22.3596595965423	1.1891306325402	18.2041596504801	6.24646467450714	1	4	7	1	30	2	26	9
-Tmem161b	-5.08032108462326	-0.818054234540908	7.69712673776783	0.0055308800357475	0.0196596078529218	0.648764565221836	8	0	0	0	0	0	0.818470924434263	1.49064397310282	2.37826126508041	0	0	0	0	0	2	2	4
-Mir463	-4.82719320612508	-1.05835510395959	7.67152298486994	0.00560990872530515	0.0198550118071565	0.349609386918062	7	0	0	0	0	0.6923364242693	1.66116728009883	0.409235462217131	0.74532198655141	0	0	0	0	2	3	1	1
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-H2-K2	-4.3739613458593	-1.53568847785942	5.4040126388066	0.0200905100485588	0.0512824876183571	0.54904969651255	5	0	0	0	0	0.34616821213465	0	1.22770638665139	0.74532198655141	0	0	0	0	1	0	3	1
-4933417D19Rik	-4.38215151610853	-1.53049991387322	5.39496611611829	0.0201949175545036	0.0514339306466265	0.565860797235032	5	0	0	0	0	0.74532198655141	1.7836959488103	0	0.694051630500793	0	0	0	0	1	3	0	1
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-Gm8615	-4.3865554457949	-1.52756030282699	5.34270773991366	0.0208091262871766	0.0527097679227499	0.602779304595555	5	0	0	0	0	0.608056135742452	0.34616821213465	1.66116728009883	0	0	0	0	0	1	1	3	0
-C730027H18Rik	-4.38660031217306	-1.52752944041572	5.3405876848061	0.0208344481447504	0.0527097679227499	0.604100547201435	5	0	0	0	0	0.74532198655141	0.594565316270102	2.10047995967078	0	0	0	0	0	1	1	3	0
-D030028A08Rik	-4.66099404649387	-1.24859807260024	5.27933372568	0.0215800044250171	0.0544301945469956	1.14292627145135	6	0	0	0	0	0.700159986556928	0	3.04028067871226	0	0	0	0	0	1	0	5	0
-Gm14403	-4.66108311409197	-1.24854214540607	5.27222466268006	0.0216683039906921	0.0544301945469956	1.1480188620546	6	0	0	0	0	0.74532198655141	0	3.50079993278464	0	0	0	0	0	1	0	5	0
-Gm3219	-4.66111058225096	-1.24852491457626	5.27002843105692	0.021695658311197	0.0544301945469956	1.14959564755902	6	0	0	0	0	0.34616821213465	0	2.04617731108566	0	0	0	0	0	1	0	5	0
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-Mir365-2	-2.40446642068728	0.656389510468249	5.25136767302149	0.0219295279997562	0.0548719110695654	0.569843581463586	25	0	0	2.43222454296981	0	5.53722426699609	1.63694184886853	2.98128794620564	1.7836959488103	0	0	4	0	10	4	4	3
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-Gm16998	-2.34605151155975	1.02476273248633	5.19737349381261	0.0226210437101954	0.0563550455749628	0.551015426306811	28	0.594565316270102	1.40031997311386	0	0.608056135742452	0.6923364242693	4.42977941359688	2.04617731108566	6.70789787896269	1	2	0	1	2	8	5	9
-Gm15850	4.32485989010306	-1.75136485782155	5.17598004331388	0.02290124934226	0.0569288137244416	0.638146949527696	4	0	2.98128794620564	0	0	0	0	0	0	0	4	0	0	0	0	0	0
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-5430405H02Rik	-2.8196995121282	0.461135729079766	5.05058855443142	0.0246175749690112	0.0597630915737058	0.75732533558914	20	0	0	0	1.40031997311386	4.16430978300476	4.86444908593961	0	2.21488970679844	0	0	0	2	6	8	0	4
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-4933404O12Rik	-4.42579132318076	-1.49815567894859	4.95531027686733	0.0260106568760744	0.0622183637224336	0.922648094486409	5	0	0	0	0	0	0	2.08215489150238	1.2161122714849	0	0	0	0	0	0	3	2
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-Gm10532	-4.2872747151629	-1.59671824839497	4.92923498677878	0.026406005013833	0.0629003167448506	0.714293128450685	5	0	0	0	0	2.08215489150238	0	0.6923364242693	0	0	0	0	0	3	0	2	0
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-Mir329	2.23803795350777	0.290422564342482	4.61558070031246	0.0316827660564916	0.0717262620445574	0.44908816914487	18	1.2161122714849	1.03850463640395	3.87605698689727	1.22770638665139	0	1.1891306325402	0	0.694051630500793	2	3	7	3	0	2	0	1
-BC029722	-4.22735989837203	-1.64150898139513	4.60640949824354	0.0318526587623106	0.0719680864312801	0.856481808302187	5	0	0	0	0	2.43222454296981	0	0.553722426699609	0	0	0	0	0	4	0	1	0
-A230108P19Rik	-2.37353765876239	0.516633701524973	4.59391725060311	0.0320856032034256	0.0723511329152344	0.586094176786546	21	0	0.608056135742452	0.34616821213465	0.553722426699609	2.45541277330279	0.74532198655141	5.35108784643091	1.40031997311386	0	1	1	1	6	1	9	2
-Snora52	-1.32770000191998	2.82430805766402	4.58495625194707	0.0322537946201336	0.0725869421332789	0.270249435101158	105	1.3846728485386	2.21488970679844	5.32006100882271	5.96257589241128	14.2695675904824	11.2025597849109	15.9631875015182	7.90472976465187	4	4	13	8	24	16	23	13
-Mir3061	1.31233812183835	3.0369942208777	4.57815474930133	0.0323820680346795	0.0727321646211995	0.278078412770089	119	7.70175985212621	13.1869809795151	20.0658524795009	6.92336424269299	6.64466912039531	4.09235462217131	2.23596595965423	6.54021847897112	11	19	33	20	12	10	3	11
-Zfp410	-2.69952260917983	0.395528824073657	4.5189405682202	0.0335215828629465	0.075143666103383	0.789500807655785	20	0	0.818470924434263	0	0	7.00159986556928	0	3.64833681445471	0.6923364242693	0	2	0	0	10	0	6	2
-Gm12359	-2.42575621884223	0.749676389218599	4.51264576021709	0.0336451587657393	0.075272796375899	0.753144082371769	26	0.608056135742452	0	1.66116728009883	0	6.70789787896269	0	7.70175985212621	1.38810326100159	1	0	3	0	9	0	11	2
-Polg2	-4.12411192811269	-1.82151885704115	4.49394057121341	0.0340151844668462	0.075803370071624	0.638146949527696	4	0	0	0	0	0	1.10744485339922	0.818470924434263	0	0	0	0	0	0	2	2	0
-Sgsm1	-4.12411192811269	-1.82151885704115	4.49394057121341	0.0340151844668462	0.075803370071624	0.638146949527696	4	0	0	0	0	0	1.38810326100159	1.2161122714849	0	0	0	0	0	0	2	2	0
-1190002F15Rik	-4.11803142846939	-1.82534652200596	4.48127406637341	0.0342681661309806	0.0759481942525399	0.638146949527696	4	0	0	0	0	0	0	1.63694184886853	0	0	0	0	0	0	0	4	0
-Tsix	-4.11803142846939	-1.82534652200596	4.48127406637341	0.0342681661309806	0.0759481942525399	0.638146949527696	4	0	0	0	0	0	0	1.3846728485386	0	0	0	0	0	0	0	4	0
-Mir542	1.05726365562716	3.91239824161194	4.48069094278527	0.0342798598072376	0.0759481942525399	0.1959886286223	225	13.6750022742123	22.4051195698217	52.0538722875595	13.3772349863339	6.92336424269299	8.30583640049414	9.41241563099402	11.1798297982712	23	32	75	22	20	15	23	15
-9230116N13Rik	-4.11133735502004	-1.8296491175196	4.4672063339432	0.0345514403378628	0.0762400644531103	0.638146949527696	4	0	0	0	0	0	0.608056135742452	0.6923364242693	0.553722426699609	0	0	0	0	0	1	2	1
-Mir297-2	-1.74036242444806	1.69583451914289	4.46707175864515	0.034554161997183	0.0762400644531103	0.412928500012421	47	2.04617731108566	0.74532198655141	1.7836959488103	0.700159986556928	7.63456793550872	3.64833681445471	5.5386913941544	2.21488970679844	5	1	3	1	11	6	16	4
-9330151L19Rik	-4.10830302209086	-1.83155766024206	4.46091717923999	0.0346788724374796	0.0762400644531103	0.638146949527696	4	0	0	0	0	0	0	1.82416840722736	0.34616821213465	0	0	0	0	0	0	3	1
-Lins	-4.10830302209086	-1.83155766024206	4.46091717923999	0.0346788724374796	0.0762400644531103	0.638146949527696	4	0	0	0	0	0	0	2.08215489150238	0.608056135742452	0	0	0	0	0	0	3	1
-4930502E09Rik	-4.09191548661964	-1.84203731318131	4.42677797549459	0.0353792352562969	0.0775760128311178	0.638146949527696	4	0	0	0	0	0	0.694051630500793	0	1.03850463640395	0	0	0	0	0	1	0	3
-Snord71	-0.955120708530058	4.51498915950296	4.4207003213376	0.0355054612538313	0.0775760128311178	0.168050833809458	341	11.891306325402	14.0031997311386	26.3739619590301	17.6336279365311	32.1936437285224	28.2398437616801	10.6401220176454	47.7006071392902	20	20	38	29	93	51	26	64
-Mir880	-4.08889162412657	-1.84393669687063	4.42056468400816	0.0355082836562712	0.0775760128311178	0.638146949527696	4	0	0	0	0	0	0	0.694051630500793	1.82416840722736	0	0	0	0	0	0	1	3
-Cd40	3.98853196498671	-1.96832823340441	4.41815303960816	0.0355585054431854	0.0775760128311178	0.638146949527696	4	0.608056135742452	0	1.66116728009883	0	0	0	0	0	1	0	3	0	0	0	0	0
-Alg11	-2.91746441789601	-0.356455446075155	4.37859552645042	0.0363929731044889	0.0788854417139366	0.706370492250227	12	0	0	0	0.700159986556928	4.85836141350555	0	1.03850463640395	0.553722426699609	0	0	0	1	7	0	3	1
-Stap2	-2.19552607597296	0.707730435297325	4.37653214141865	0.0364370588531311	0.0788854417139366	0.570956875691062	25	0	1.1891306325402	1.40031997311386	0	6.08056135742452	0.34616821213465	3.32233456019766	1.63694184886853	0	2	2	0	10	1	6	4
-Mir129-1	-4.06884099363945	-1.85841131947687	4.37629201354318	0.0364421929934367	0.0788854417139366	0.638146949527696	4	0	0	0	0	0.608056135742452	0.34616821213465	1.10744485339922	0	0	0	0	0	1	1	2	0
-A730020M07Rik	-4.06582213619695	-1.86030123418635	4.3701612498462	0.0365735308209224	0.0788854417139366	0.638146949527696	4	0	0	0	0	0.34616821213465	0	1.22770638665139	0	0	0	0	0	1	0	3	0
-F630206G17Rik	-4.06582213619695	-1.86030123418635	4.3701612498462	0.0365735308209224	0.0788854417139366	0.638146949527696	4	0	0	0	0	0.594565316270102	0	2.08215489150238	0	0	0	0	0	1	0	3	0
-Gm21944	-4.06582213619695	-1.86030123418635	4.3701612498462	0.0365735308209224	0.0788854417139366	0.638146949527696	4	0	0	0	0	0.553722426699609	0	2.23596595965423	0	0	0	0	0	1	0	3	0
-4930451G09Rik	-4.06218135011626	-1.86266730759621	4.36262408960627	0.0367356769979684	0.0789367372027908	0.638146949527696	4	0	0	0	0	0.34616821213465	1.10744485339922	0	0.74532198655141	0	0	0	0	1	2	0	1
-4933421O10Rik	-4.06218135011626	-1.86266730759621	4.36262408960627	0.0367356769979684	0.0789367372027908	0.638146949527696	4	0	0	0	0	0.34616821213465	1.10744485339922	0	0.74532198655141	0	0	0	0	1	2	0	1
-1700034P13Rik	-4.05615312273869	-1.86643936217435	4.35042607968738	0.0369996883643231	0.0791333136258031	0.638146949527696	4	0	0	0	0	0.594565316270102	0	1.38810326100159	0.608056135742452	0	0	0	0	1	0	2	1
-Fam120aos	-4.05615312273869	-1.86643936217435	4.35042607968738	0.0369996883643231	0.0791333136258031	0.638146949527696	4	0	0	0	0	0.694051630500793	0	0.6923364242693	0.553722426699609	0	0	0	0	1	0	2	1
-Ythdf3	-1.74609152248204	1.80381807875995	4.34879124911614	0.0370352230290787	0.0791333136258031	0.451143612970826	52	1.3846728485386	0.553722426699609	1.63694184886853	1.49064397310282	9.51304506032163	2.10047995967078	13.1869809795151	1.82416840722736	4	1	4	2	16	3	19	3
-Gm10516	-4.04950853481582	-1.87068223831354	4.33686580917984	0.0372955180993558	0.0795266882692114	0.638146949527696	4	0	0	0	0	0.553722426699609	0.409235462217131	0	1.1891306325402	0	0	0	0	1	1	0	2
-Mir294	-4.04650119827995	-1.87256292336199	4.33081029928285	0.0374284238392345	0.0795266882692114	0.638146949527696	4	0	0	0	0	0.594565316270102	0	0.694051630500793	1.2161122714849	0	0	0	0	1	0	1	2
-Snora70	-4.04650119827995	-1.87256292336199	4.33081029928285	0.0374284238392345	0.0795266882692114	0.638146949527696	4	0	0	0	0	0.608056135742452	0	0.553722426699609	0.818470924434263	0	0	0	0	1	0	1	2
-C530005A16Rik	-2.35830413614665	0.0398009444546594	4.29264896394365	0.0382774838415955	0.0811795707495549	0.464336618201745	15	0	0.694051630500793	0	0.34616821213465	2.76861213349805	0.409235462217131	2.98128794620564	1.7836959488103	0	1	0	1	5	1	4	3
-2310044G17Rik	-2.26269892849728	0.549698073149406	4.2847771464391	0.0384551234624672	0.0814050016153526	0.561232526625958	21	0	1.2161122714849	0	0.553722426699609	2.45541277330279	2.23596595965423	4.16195721389071	1.40031997311386	0	2	0	1	6	3	7	2
-2610020C07Rik	-2.70163097892754	0.364000305555862	4.2653219113525	0.0388978785475462	0.0817329391154928	0.871328639864001	19	1.38810326100159	0	0	0	2.86464823551992	0	5.35108784643091	0.700159986556928	2	0	0	0	7	0	9	1
-Snhg3	-1.41622896880049	2.6340659540425	4.26330501043091	0.0389440832520463	0.0817329391154928	0.335657556826962	94	6.30143987901235	1.38810326100159	6.08056135742452	1.03850463640395	15.5042279475891	2.45541277330279	13.4157957579254	10.7021756928618	9	2	10	3	28	6	18	18
-1500015L24Rik	-4.01381917958462	-1.89488966537583	4.26225317431253	0.0389682023477897	0.0817329391154928	0.638146949527696	4	0	0	0	0	1.2161122714849	0	1.10744485339922	0	0	0	0	0	2	0	2	0
-Cyp2d37-ps	-4.01381917958462	-1.89488966537583	4.26225317431253	0.0389682023477897	0.0817329391154928	0.638146949527696	4	0	0	0	0	1.38810326100159	0	0.6923364242693	0	0	0	0	0	2	0	2	0
-Trpt1	-4.01381917958462	-1.89488966537583	4.26225317431253	0.0389682023477897	0.0817329391154928	0.638146949527696	4	0	0	0	0	1.10744485339922	0	1.49064397310282	0	0	0	0	0	2	0	2	0
-4833417C18Rik	-2.70825404396028	-0.725970783957293	4.25732760148008	0.0390813566696084	0.0818198678165563	0.428193962550269	9	0	0	0.34616821213465	0	0.818470924434263	0.74532198655141	0.594565316270102	2.80063994622771	0	0	1	0	2	1	1	4
-5730408K05Rik	-4.00720956832825	-1.89909188977037	4.24903440378983	0.0392726541017003	0.0820697771612455	0.638146949527696	4	0	0	0	0	1.40031997311386	0.694051630500793	0	0.34616821213465	0	0	0	0	2	1	0	1
-BC031361	-4.00422113245092	-1.90095362347432	4.24313587364672	0.0394093118010205	0.0822047984734266	0.638146949527696	4	0	0	0	0	1.1891306325402	0	0.694051630500793	0.608056135742452	0	0	0	0	2	0	1	1
-Yipf2	-3.34184791158038	-0.252874288421611	4.22074958507356	0.0399325160996857	0.0828118071394653	1.30930817659146	12	0	0	0.700159986556928	0	0.608056135742452	0	5.53722426699609	0	0	0	1	0	1	0	10	0
-1700102H20Rik	3.89082017977606	-2.03056170835189	4.21828219859005	0.0399906272864552	0.0828118071394653	0.638146949527696	4	0	0	1.3846728485386	0	0	0	0	0	0	0	4	0	0	0	0	0
-9230112J17Rik	3.89082017977606	-2.03056170835189	4.21828219859005	0.0399906272864552	0.0828118071394653	0.638146949527696	4	0	0	2.43222454296981	0	0	0	0	0	0	0	4	0	0	0	0	0
-Mir3100	3.89082017977606	-2.03056170835189	4.21828219859005	0.0399906272864552	0.0828118071394653	0.638146949527696	4	0	0	2.43222454296981	0	0	0	0	0	0	0	4	0	0	0	0	0
-Cops5	-2.74277299547302	0.226431665149612	4.18235809780445	0.040846829713992	0.0843223691619662	0.93474486502049	18	0.553722426699609	0	0.74532198655141	0	5.60127989245543	0	4.86444908593961	0	1	0	1	0	8	0	8	0
-Mir338	0.880044436101206	5.05378388813902	4.17709516231065	0.0409738719926891	0.0843223691619662	0.157817687637039	469	43.4099191665296	37.4787880470428	54.7250522168207	29.0781298193106	33.7770680286762	21.2802440352908	9.68918582516833	31.5119617623154	62	54	90	84	61	52	13	53
-2010003O02Rik	-2.26499437181878	0.173533443670672	4.17505423403297	0.0410232496648664	0.0843223691619662	0.553877020535981	17	0	0	1.7836959488103	0	2.08215489150238	1.2161122714849	2.0770092728079	1.66116728009883	0	0	3	0	3	2	6	3
-Snora61	-1.13929292635118	3.42314387958311	4.17384160983589	0.0410526171619562	0.0843223691619662	0.235971517375169	164	7.00159986556928	3.47025815250396	13.9852911220764	3.80785033348115	27.6861213349805	8.59394470655976	17.8877276772338	11.891306325402	10	5	23	11	50	21	24	20
-Mir3065	0.880052068574874	5.05379134091003	4.17231570109871	0.0410896032025006	0.0843223691619662	0.158022076718089	469	25.3725986574621	40.2473872737761	53.5108784643091	58.813438870782	42.3371494605484	31.6189190586075	4.50018675775045	29.3472886150793	62	54	90	84	61	52	13	53
-Mir465	-3.96505397297716	-1.92726105726275	4.16328361615134	0.0413092470664329	0.0846209172402154	0.638146949527696	4	0	0	0	0	2.10047995967078	0.694051630500793	0	0	0	0	0	0	3	1	0	0
-4930414N06Rik	-3.9620867245947	-1.929103668579	4.15754091127589	0.0414495402538273	0.084651135570796	0.638146949527696	4	0	0	0	0	1.7836959488103	0	0.694051630500793	0	0	0	0	0	3	0	1	0
-Mir467d	2.05279780631616	0.848429956164326	4.15660795974648	0.0414723793024321	0.084651135570796	0.56454176739212	27	2.97282658135051	1.40031997311386	7.63456793550872	2.43222454296981	0	0	0.409235462217131	2.98128794620564	5	2	11	4	0	0	1	4
-D930015M05Rik	-2.28826976055491	0.444390421848186	4.15285346786993	0.0415644245963214	0.0846875151150048	0.610024792932182	20	0	0.594565316270102	0.700159986556928	0.694051630500793	3.64833681445471	0.34616821213465	4.98350184029649	0.409235462217131	0	1	1	1	6	1	9	1
-Mea1	-2.26984916965905	-0.17311453854932	4.13558639294138	0.0419905169624685	0.085403172645591	0.384698019815479	13	0.409235462217131	0	0.594565316270102	0	2.08215489150238	1.2161122714849	1.3846728485386	1.10744485339922	1	0	1	0	3	2	4	2
-C920021L13Rik	-1.96158632640905	1.14195272250258	4.11494573036799	0.0425058889106721	0.086297543144265	0.536329402383485	32	0	0.818470924434263	1.49064397310282	1.1891306325402	4.20095991934157	0.694051630500793	6.08056135742452	3.11551390921185	0	2	2	2	6	1	10	9
-2810013P06Rik	-2.35851702389742	-0.221303845666127	4.10700942780947	0.0427058146741521	0.0865494396859813	0.481368760572018	13	0	0	1.2161122714849	0	2.21488970679844	1.63694184886853	1.49064397310282	0.594565316270102	0	0	2	0	4	4	2	1
-Snhg10	-2.71050155843518	-0.5701353917104	4.10375519077588	0.0427880787236106	0.0865624074887228	0.522207025512832	10	0.74532198655141	0	0	0	2.43222454296981	0	1.10744485339922	1.22770638665139	1	0	0	0	4	0	2	3
-Scarna13	-2.71013588698149	-0.570227672567595	4.09436542619313	0.0430263785049904	0.0868904387153877	0.525354151245509	10	0.553722426699609	0	0	0	2.80063994622771	0	1.2161122714849	1.03850463640395	1	0	0	0	4	0	2	3
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-D130009I18Rik	-2.0187475113017	-0.082035836636512	2.6163583191924	0.105766924195447	0.177732047874824	0.833114006854998	15	0	0	1.03850463640395	0	2.45541277330279	3.72660993275705	0.594565316270102	0	0	0	3	0	6	5	1	0
-1110054M08Rik	-1.87542361955477	0.0936957172998474	2.59539737265037	0.107174556211294	0.179832600936892	0.660615985328115	16	0.608056135742452	0	0.553722426699609	0.409235462217131	4.47193191930846	0	4.20095991934157	0.694051630500793	1	0	1	1	6	0	6	1
-Mir5128	-1.85501263716432	0.396993446538296	2.59009971500331	0.107533565631489	0.180170041682127	0.753196269796778	20	0	0	1.40031997311386	1.38810326100159	4.25639295019716	0	4.42977941359688	0.409235462217131	0	0	2	2	7	0	8	1
-9330175M20Rik	1.84328988974851	-0.684609520356453	2.58030052193028	0.108201117766631	0.181022691160889	0.333995814209591	9	1.49064397310282	1.1891306325402	1.40031997311386	0.694051630500793	0.608056135742452	0	0	0.409235462217131	2	2	2	1	1	0	0	1
-Mir339	-0.581232897852849	5.31251654804454	2.56028969456141	0.109578502195027	0.183058669113508	0.111413713845571	599	15.550947564251	27.5769135024022	62.4293582083607	36.4083193009603	99.9434347921142	52.9008838095933	24.5779430615601	35.9919577354746	38	37	105	52	144	87	71	65
-Rnu73b	-1.30715431594542	1.54023730915002	2.5449412389762	0.110648027427511	0.184575145167822	0.416283885552946	44	1.10744485339922	1.22770638665139	2.23596595965423	1.7836959488103	12.6028797580247	1.38810326100159	4.86444908593961	1.73084106067325	2	3	3	3	18	2	8	5
-1500011K16Rik	-2.44477877849851	-1.04999173389295	2.52063479978018	0.112365342920624	0.187166213536397	0.922990651986708	7	0	0	0.34616821213465	0	0	0	2.37826126508041	1.40031997311386	0	0	1	0	0	0	4	2
-Kat5	-2.06663127669773	-0.189588133971375	2.51404645283263	0.112835867601293	0.187675983867457	0.781443612530342	12	0	0.694051630500793	0	0.34616821213465	0.553722426699609	1.63694184886853	3.72660993275705	0	0	1	0	1	1	4	5	0
-9530026P05Rik	1.64356923703615	0.54790279121103	2.50755199185487	0.113301812428464	0.188176663727623	0.583510200246358	20	2.08215489150238	2.43222454296981	1.3846728485386	2.21488970679844	0	0.74532198655141	2.37826126508041	0	3	4	4	4	0	1	4	0
-BC090627	1.25248432027161	1.77408019310546	2.49880717121329	0.113932562366748	0.188745903156683	0.419415630888235	47	1.63694184886853	8.94386383861692	3.56739189762061	6.30143987901235	4.85836141350555	0.608056135742452	0.6923364242693	3.32233456019766	4	12	6	9	7	1	2	6
-Cep57	-2.46722583600765	-0.784380325003353	2.49821524958084	0.113975396384711	0.188745903156683	1.04274664639639	8	0.553722426699609	0	0	0	0	0	3.04028067871226	0.6923364242693	1	0	0	0	0	0	5	2
-Mir29b-2	1.30899912808112	1.42150410550797	2.49032016025445	0.114548420468998	0.189419924282792	0.437871544069771	41	2.10047995967078	3.47025815250396	9.12084203613678	2.0770092728079	2.76861213349805	0	1.49064397310282	2.97282658135051	3	5	15	6	5	0	2	5
-Snhg6	-0.514505510013689	6.93280384212585	2.4763014027307	0.115573746552834	0.190731659755944	0.0972226574445347	1762	86.2119708591647	96.6220781448561	132.563861425651	116.138721926808	135.005602732513	130.678492701108	104.764278327586	160.244227108553	145	138	191	191	390	236	256	215
-9430091E24Rik	-1.44502141414246	1.54308552766239	2.47491096362017	0.115675993471615	0.190731659755944	0.562785698427756	42	1.10744485339922	0.818470924434263	1.49064397310282	2.37826126508041	7.00159986556928	0	9.72889817187923	2.0770092728079	2	2	2	4	10	0	16	6
-1810062O18Rik	-2.23597145760443	-1.01516117709593	2.46991383953216	0.116044285629445	0.191062813713127	0.594087095383153	7	0.34616821213465	0	0	0	0.594565316270102	1.40031997311386	2.08215489150238	0	1	0	0	0	1	2	3	0
-Snord87	-0.512780624035546	6.93050794589746	2.46222476957477	0.116613507673046	0.191723360597904	0.0971145746784507	1759	88.1681396826555	47.7712132745817	105.207261072926	78.1639732834721	290.67557475505	139.722849323474	178.540796572017	149.22110055767	145	138	190	191	390	235	255	215
-9330179D12Rik	1.32807407979619	1.55993572794472	2.4552866999784	0.117129780781099	0.192205234250727	0.466439067678837	40	4.20095991934157	4.16430978300476	4.25639295019716	3.11551390921185	0	1.22770638665139	2.23596595965423	3.56739189762061	6	6	7	9	0	3	3	6
-Flcn	-1.69566681237587	0.535039416014445	2.45314978559534	0.11728930033472	0.192205234250727	0.67404503956276	22	0	0.34616821213465	1.66116728009883	0.409235462217131	5.21725390585987	1.1891306325402	5.60127989245543	0	0	1	3	1	7	2	8	0
-0610009L18Rik	1.58608108196201	0.372203685365149	2.45150880460495	0.117411961676386	0.192205234250727	0.541718588209175	21	1.40031997311386	1.38810326100159	6.68861749316697	0.34616821213465	1.66116728009883	0	0.74532198655141	0.594565316270102	2	2	11	1	3	0	1	1
-Gabpb1	-2.21446880991551	-1.02828360655136	2.44120077582773	0.118185724551529	0.193194715921625	0.580001149839739	7	0	0	0	0.34616821213465	0.553722426699609	0	2.23596595965423	1.1891306325402	0	0	0	1	1	0	3	2
-Clk1	-1.50255113323922	1.80316637211895	2.43735377159324	0.118475939628736	0.193392055960498	0.690768297461704	54	3.64833681445471	0	4.42977941359688	0	11.9251517848226	0	12.6028797580247	4.16430978300476	6	0	8	0	16	0	18	6
-Wdr13	1.66976242845857	-0.285618792288445	2.42653830982369	0.119296081575707	0.194452612968402	0.402030823193521	12	0.6923364242693	0.553722426699609	1.22770638665139	2.23596595965423	1.1891306325402	0	0.694051630500793	0	2	1	3	3	2	0	1	0
-Mir363	-2.04530975161902	-0.169477227326255	2.41704233957579	0.120021347056309	0.195355716107344	0.83068581203153	13	0	1.10744485339922	0	0	2.37826126508041	0	0.694051630500793	3.64833681445471	0	2	0	0	4	0	1	6
-Mir2137	2.42315770170727	-1.17092319864775	2.41285706654857	0.120342550605879	0.195599501768245	0.962843156656157	6	0.818470924434263	0	0	2.10047995967078	0.694051630500793	0	0	0	2	0	0	3	1	0	0	0
-Mir1839	-0.534183367388678	6.73673012730561	2.40554710265568	0.120905847898993	0.196235522692391	0.108147846884193	1655	46.652842692753	55.8991489913558	247.339171568362	67.2153587094651	208.909540780739	111.274272840869	84.4650437608545	125.141268434112	114	75	416	96	301	183	244	226
-Gm10125	2.22437962369311	-1.21927187008007	2.39807781484729	0.121484441143166	0.196691035893343	0.587276574265586	6	1.10744485339922	0.818470924434263	0.74532198655141	0	0	0	0.608056135742452	0	2	2	1	0	0	0	1	0
-Zfp326	-1.63611428275883	0.346273936896955	2.39696460511976	0.121570936088169	0.196691035893343	0.550744863081575	19	1.1891306325402	0.700159986556928	0.694051630500793	0	2.42317748494255	0	1.63694184886853	2.98128794620564	2	1	1	0	7	0	4	4
-4930417O13Rik	-1.9945649280459	-0.258441456807758	2.39525817691125	0.121703655863891	0.196691035893343	0.747013546169459	12	1.40031997311386	0	0	0	1.66116728009883	0	3.72660993275705	1.1891306325402	2	0	0	0	3	0	5	2
-AF357359	1.29026542084414	1.77790507271985	2.38693456277286	0.122353342936739	0.197269068918764	0.496501200687077	55	5.35108784643091	0.700159986556928	15.9631875015182	3.64833681445471	3.4616821213465	2.21488970679844	0.818470924434263	0	9	1	23	6	10	4	2	0
-Elmo1	2.15124893872068	-1.28123993933874	2.38624804142815	0.122407099732239	0.197269068918764	0.463249530709569	6	0.409235462217131	1.49064397310282	1.1891306325402	0	0	0	0	0.553722426699609	1	2	2	0	0	0	0	1
-Asb7	-2.30332380737985	-1.13517358872786	2.37979511991411	0.122913666092021	0.197806055022561	0.786898494565176	7	0	0	0.34616821213465	0	1.22770638665139	0	1.7836959488103	0	0	0	1	0	3	0	3	0
-Mir744	-0.52498904749871	7.1362287941672	2.36085310667998	0.124414134487684	0.199938771056968	0.107589691134598	2175	51.2328953959282	73.0913603243484	208.710085730737	87.202672426515	261.014173842575	224.051195698217	129.787654903648	195.794075709069	148	132	510	117	439	320	187	322
-6720401G13Rik	-2.65953479134889	-0.584180947981368	2.3525835050485	0.125075568735887	0.200719020995285	1.61181893425389	9	0	0	0	0.608056135742452	0	0	3.27388369773705	0	0	0	0	1	0	0	8	0
-Gm11602	-1.29756714405707	2.01010378357763	2.34451013262115	0.125725078502831	0.201477969904116	0.519415721978893	61	0	1.3846728485386	3.32233456019766	2.45541277330279	16.397083704131	1.7836959488103	12.6028797580247	1.38810326100159	0	4	6	6	22	3	18	2
-Snora74a	1.33264355338965	1.25318029683733	2.33695526841141	0.126336270684184	0.202173471038785	0.483100717105593	36	0.6923364242693	2.76861213349805	4.50159008438844	5.21725390585987	4.16195721389071	0	1.38810326100159	1.2161122714849	2	5	11	7	7	0	2	2
-2900056M20Rik	1.89186552248576	-0.574049734117164	2.33244151001062	0.126703012044797	0.202476381993156	0.588820779961853	10	1.38810326100159	1.2161122714849	1.3846728485386	0	0	0	0	1.40031997311386	2	2	4	0	0	0	0	2
-Gm14872	-2.23735510374369	-1.00614089551379	2.32239133209804	0.127523846951547	0.203503090030371	0.720120448365452	7	0.594565316270102	0	0	0	0.34616821213465	2.21488970679844	0.409235462217131	0	1	0	0	0	1	4	1	0
-2900076A07Rik	-0.521545176134999	6.74529850321175	2.30997114204509	0.128546436531987	0.204848441456699	0.107375020056288	1663	40.1555126076194	42.6366268558699	170.651187744544	72.2962326954868	178.964160197301	128.129277539918	170.736701103195	137.420686677794	116	77	417	97	301	183	246	226
-1700011J10Rik	-1.72849334751898	0.640580677413143	2.29973642498749	0.129395954814459	0.20591462265453	0.796092222115673	22	0.6923364242693	0	0.818470924434263	0.74532198655141	0.594565316270102	6.30143987901235	0	4.25639295019716	2	0	2	1	1	9	0	7
-Snhg4	1.10541905914778	1.69573600781149	2.28324904354064	0.130777656190338	0.207823545561526	0.330995408402855	47	1.63694184886853	4.47193191930846	6.54021847897112	7.00159986556928	4.85836141350555	1.82416840722736	1.03850463640395	1.66116728009883	4	6	11	10	7	3	3	3
-Mir3086	1.49810597458547	0.00644830414200601	2.27986633946565	0.131063168287593	0.20798758694874	0.379947811715574	15	1.1891306325402	1.40031997311386	3.47025815250396	1.2161122714849	0.6923364242693	0	0.409235462217131	0.74532198655141	2	2	5	2	2	0	1	1
-Snord15b	-0.79305867858917	3.87885497090033	2.2770370697661	0.131302502667252	0.208077993810187	0.221656978878816	219	14.3967830941898	6.5477673954741	17.8877276772338	4.16195721389071	44.1100791530865	16.657239132019	15.2014033935613	11.7697192125781	26	16	24	7	63	24	25	34
-Adamts10	-2.12723975853336	-0.535083741337976	2.24662969356018	0.133905766378689	0.211909125434236	1.02278601950861	10	0	0	1.1891306325402	0	0	2.43222454296981	1.3846728485386	0	0	0	2	0	0	4	4	0
-Brd2	-1.18642173245467	1.77815650748116	2.24291767379786	0.134227493599469	0.21212405844459	0.418486210030943	52	2.77620652200317	2.43222454296981	2.42317748494255	0	6.13853193325697	1.49064397310282	5.94565316270102	7.00159986556928	4	4	7	0	15	2	10	10
-2310050B05Rik	1.87730148304571	-0.58167432047207	2.22996997764389	0.135356477771014	0.213612366717465	0.634568295148245	10	0.74532198655141	0	2.80063994622771	2.08215489150238	0	0	0	0.818470924434263	1	0	4	3	0	0	0	2
-Mir300	0.931234363214763	3.8186971624929	2.22279374259378	0.135986788643579	0.214310671052933	0.331226170767854	222	13.3772349863339	6.2310278184237	39.8680147223719	11.8678284042968	39.5020652872247	11.891306325402	1.40031997311386	4.16430978300476	22	18	72	29	53	20	2	6
-Mphosph9	-2.09978232493943	-1.10329984032928	2.18617729120828	0.13925454794207	0.219157847175037	0.588884758294567	7	0	0	0	0.694051630500793	2.43222454296981	0.34616821213465	0	0.409235462217131	0	0	0	1	4	1	0	1
-4930509E16Rik	-1.96670064589673	-0.445192289297211	2.17161954354077	0.140578116453461	0.220659695801666	0.831201671482097	11	0	0	0.700159986556928	0.694051630500793	2.43222454296981	1.73084106067325	0	0	0	0	1	1	4	5	0	0
-Mir103-2	-0.941836722508497	2.47294225074852	2.17142809105701	0.140595616869247	0.220659695801666	0.278613498393072	81	4.25639295019716	2.0770092728079	4.98350184029649	1.63694184886853	12.670473771374	5.94565316270102	9.10207982524007	10.4107744575119	7	6	9	4	17	10	13	15
-Snord49a	-0.501332616501719	6.17482047891014	2.16504808635641	0.141180206533623	0.221095374572332	0.103259611976917	1114	51.0767154023659	17.6545788188671	141.7529412351	30.6926596662849	172.914700879927	89.7793627567853	84.0191983868314	100.637486422615	84	51	256	75	232	151	120	145
-Srsf3	-1.12110428542334	2.04712487958043	2.16417127282267	0.141260760791613	0.221095374572332	0.39021138949617	57	0.818470924434263	5.96257589241128	1.1891306325402	2.80063994622771	4.85836141350555	6.68861749316697	3.11551390921185	7.75211397379453	2	8	2	4	7	11	9	14
-Gm5512	-1.86047883743836	-0.34231156915842	2.16163853408758	0.14149373775901	0.221156650387713	0.691171162327006	12	0.694051630500793	0.608056135742452	0	0	2.86464823551992	0	1.1891306325402	0.700159986556928	1	1	0	0	7	0	2	1
-Snord73a	-1.11940214938228	2.03915188884629	2.15781877008791	0.141845920487471	0.221403823907256	0.4040626562047	64	2.08215489150238	1.82416840722736	2.42317748494255	2.76861213349805	11.8678284042968	4.47193191930846	5.35108784643091	1.40031997311386	3	3	7	5	29	6	9	2
-Mir1934	1.83947282188827	-0.74446424423774	2.14056139117466	0.143449388374919	0.223600754283857	0.590912312839328	9	2.10047995967078	0.694051630500793	1.82416840722736	0	1.10744485339922	0	0	0	3	1	3	0	2	0	0	0
-Adam17	-1.47765485817054	0.572656985101098	2.13830311141108	0.143660721117262	0.22362466956998	0.53793072464044	22	0	1.38810326100159	0.608056135742452	0.6923364242693	4.42977941359688	0.409235462217131	3.72660993275705	1.7836959488103	0	2	1	2	8	1	5	3
-Mir484	0.496724159779706	7.15300390847319	2.1270083709805	0.144722972074943	0.224971268579713	0.106862047953958	2052	199.746292395778	133.182630844503	295.467514327024	166.57239132019	173.295998686599	77.5416795181615	55.9259650966606	117.859813118534	268	224	422	240	285	224	101	288
-Mir211	-2.11640411296348	-1.296635198523	2.11559632877154	0.145805249833451	0.226345292598596	0.598280443421084	6	0	0	0.409235462217131	0	0.594565316270102	2.10047995967078	0.694051630500793	0	0	0	1	0	1	3	1	0
-Pradc1	-2.25590005990977	-0.95868629848959	2.10291632826993	0.147018491652324	0.227918612738182	0.976906978836214	7	0	0.553722426699609	0	0	0	1.40031997311386	2.77620652200317	0	0	1	0	0	0	2	4	0
-Gm11974	-1.81523971179377	-0.398341440836169	2.09115275386919	0.148154242220698	0.229104045846039	0.642388867011053	11	0.694051630500793	0.608056135742452	0	0	1.22770638665139	0.74532198655141	0	3.50079993278464	1	1	0	0	3	1	0	5
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-Mir29c	0.439813587022935	8.65700369906282	1.60008315656274	0.205891426634024	0.296244789141767	0.114326748769424	6038	268.049227752221	430.796108226715	869.849057703159	467.006711033471	744.717399527351	379.42702870329	84.8112119729892	405.878538770814	655	578	1463	667	1073	624	245	733
-Mir154	1.37960167534945	0.268938119088842	1.59784572324499	0.206208770512373	0.296327716819418	0.67170911506608	18	1.40031997311386	0	3.64833681445471	1.73084106067325	1.10744485339922	1.22770638665139	0	0	2	0	6	5	2	3	0	0
-Mir199a-1	-1.25392839099751	0.291496171629457	1.58983405656815	0.207349844106049	0.297592669339624	0.468211338277266	18	1.22770638665139	0	1.1891306325402	0	2.77620652200317	1.2161122714849	1.3846728485386	1.66116728009883	3	0	2	0	4	2	4	3
-Snora21	-1.17880510125088	0.448908358278964	1.58111566715797	0.20860006382576	0.299010895509035	0.417794509705249	20	1.2161122714849	0	1.66116728009883	0.409235462217131	2.23596595965423	2.37826126508041	2.80063994622771	2.08215489150238	2	0	3	1	3	4	4	3
-Abhd11	-1.60388335035277	-0.886424341832775	1.574095603599	0.209613228289782	0.30008619006103	0.565524102859339	8	0	0	0.818470924434263	0	0	1.40031997311386	1.38810326100159	1.2161122714849	0	0	2	0	0	2	2	2
-Airn	1.27888007861366	2.32523714626309	1.55337658209858	0.212637657382994	0.304034545205509	0.862049740104597	66	2.80063994622771	12.4929293490143	7.29667362890942	4.1540185456158	0	0	14.9064397310282	0	4	18	12	12	0	0	20	0
-Etohd2	-1.89099714221186	-1.26888157123423	1.54618221365326	0.213699935678948	0.30517099700836	0.807100498203147	6	0	0.409235462217131	0	0	1.40031997311386	0	1.82416840722736	0	0	1	0	0	2	0	3	0
-Mir410	0.666784938679241	3.81377700524501	1.54417074996869	0.213998063476999	0.305214738034069	0.23496414574264	208	8.30803709123159	18.2728400810871	19.2340667242052	12.670473771374	26.7554392321546	14.7033597176955	6.24646467450714	7.29667362890942	24	33	47	17	45	21	9	12
-Mir101c	-1.75549972402918	-1.57397914791002	1.50511614966304	0.219885833746325	0.313220644574978	0.411688585331216	5	0	0	0.608056135742452	0	0.553722426699609	0	1.49064397310282	0.594565316270102	0	0	1	0	1	0	2	1
-Pisd-ps3	-1.33389895984124	0.00672166916161362	1.50012941739273	0.220651450015256	0.313919332253624	0.563932680512065	15	0.34616821213465	0.553722426699609	0.818470924434263	0	2.37826126508041	0	3.47025815250396	1.2161122714849	1	1	2	0	4	0	5	2
-Spns1	-1.53226254772568	-0.777230696562665	1.471774189655	0.225065975054855	0.319801092823898	0.588376948844574	9	0	0	0.700159986556928	0.694051630500793	3.04028067871226	0.34616821213465	0.553722426699609	0	0	0	1	1	5	1	1	0
-Mir3068	0.531849077504373	4.76804304935561	1.46182454798486	0.226640039088934	0.321637169901086	0.165206189188114	431	27.9445698646948	22.4051195698217	104.80179620562	16.4175156650462	25.9626159100987	18.8265625077867	14.7324766398167	21.6143376099909	47	32	151	27	75	34	36	29
-Fbxo34	-1.26134769200218	0.0511572593766371	1.44298374739789	0.229657114922446	0.325513997672685	0.485854325295224	15	0.700159986556928	0.694051630500793	0.608056135742452	0.34616821213465	2.21488970679844	1.22770638665139	2.98128794620564	0	1	1	1	1	4	3	4	0
-Alg9	-1.67710411612717	-0.486610304387977	1.43852873805825	0.230377571035755	0.326130035424065	0.983998012965562	10	0.608056135742452	0.34616821213465	0	0	1.49064397310282	0	4.20095991934157	0	1	1	0	0	2	0	6	0
-Magix	-1.88370283372871	-1.54126907941154	1.43478739992785	0.230984718555754	0.326584341848966	0.843905991108154	5	0	0	0.74532198655141	0	0	0.694051630500793	1.82416840722736	0	0	0	1	0	0	1	3	0
-Cnot2	-1.38950438484497	0.419878833526545	1.41797410139312	0.233737144029816	0.330066932349035	0.854348862504364	21	0	1.40031997311386	1.38810326100159	0.608056135742452	3.80785033348115	0	2.04617731108566	0	0	2	2	1	11	0	5	0
-1700061I17Rik	1.75488222529044	-1.65609647528833	1.41137265247084	0.234828658741623	0.331198392613339	0.605410820788776	5	0	0	2.08215489150238	0.608056135742452	0.34616821213465	0	0	0	0	0	3	1	1	0	0	0
-Gm10865	-1.48057581752313	-0.841523480449415	1.40943286547085	0.235150563602662	0.331242954408194	0.492084716551793	8	0	0	0.594565316270102	0.700159986556928	0	1.2161122714849	0.6923364242693	1.10744485339922	0	0	1	1	0	2	2	2
-Snord83b	-0.576387059675669	3.89404617232097	1.39650694760333	0.237309298047112	0.333738123904012	0.188423727901865	221	15.4035197042524	8.32861956600951	21.2819647509858	5.5386913941544	26.5786764815813	9.00318016877689	25.3409475427479	19.0260901206433	22	12	35	16	48	22	34	32
-Orc6	-1.65891001544319	-1.53143456249569	1.39410757284254	0.237712651897134	0.333738123904012	0.346829941720672	5	0.553722426699609	0	0	0	0.700159986556928	0.694051630500793	0.608056135742452	0.34616821213465	1	0	0	0	1	1	1	1
-Nnt	-0.943384996373025	3.06429209846151	1.3928418650093	0.237925762385849	0.333738123904012	0.530661278894176	121	7.63456793550872	6.08056135742452	2.42317748494255	4.42977941359688	14.3232411775996	0	26.1608739158845	4.20095991934157	11	10	7	8	35	0	44	6
-1700113A16Rik	-1.25132935558282	-0.405410492935541	1.39185622273126	0.238091878052468	0.333738123904012	0.335679278399479	11	0.74532198655141	0	0.700159986556928	0.694051630500793	1.2161122714849	0.34616821213465	1.10744485339922	1.22770638665139	1	0	1	1	2	1	2	3
-Snord111	-0.768354560924835	2.44255708268487	1.37937795879974	0.240207131983939	0.336289984777514	0.302987417663513	82	4.20095991934157	2.77620652200317	7.90472976465187	2.0770092728079	12.735615814091	5.72929647103984	7.4532198655141	3.56739189762061	6	4	13	6	23	14	10	6
-Mir377	1.61685029109297	-0.764927019547182	1.3719133201312	0.241483420704625	0.337338320076739	0.871922904191011	8	0.34616821213465	0	0.409235462217131	2.98128794620564	0	1.40031997311386	0	0	1	0	1	4	0	2	0	0
-Gm6793	-1.78278223738427	-1.33945983784321	1.37154128636168	0.241547245839348	0.337338320076739	0.822180880884212	6	0	0.34616821213465	0	0	2.98128794620564	0	0.700159986556928	0	0	1	0	0	4	0	1	0
-H2-T10	-1.81297627715528	-1.58069385552309	1.36343872090317	0.242942409193657	0.338871991308023	0.783950373546019	5	0	0	0.74532198655141	0	0.700159986556928	0	1.82416840722736	0	0	0	1	0	1	0	3	0
-Ubl4	-1.27034177587966	0.0534863754405797	1.3565087782031	0.244143458366216	0.340131484732421	0.571194645489501	15	0.34616821213465	0	0.409235462217131	1.49064397310282	1.7836959488103	0	3.47025815250396	1.82416840722736	1	0	1	2	3	0	5	3
-Mirlet7a-1	-0.479655320722763	4.78553688143684	1.34788689468875	0.24564787267199	0.341810027705781	0.142907204927484	419	17.6336279365311	8.30803709123159	49.2812959762652	13.0955347909482	61.861724883767	34.4847883436659	25.2057595160494	47.1955108740539	29	24	89	32	83	58	36	68
-Gm2518	-1.39162129449246	-0.884936739010693	1.34396740253008	0.246335518812973	0.342349362930088	0.381243283650106	8	0	0.74532198655141	0.594565316270102	0	1.38810326100159	0	0.6923364242693	1.10744485339922	0	1	1	0	2	0	2	2
-Minos1	-1.18883665303021	0.474780827930178	1.32978558037784	0.248843366833975	0.345413967831588	0.613575613139105	22	0.594565316270102	1.40031997311386	2.08215489150238	0	3.80785033348115	0.553722426699609	0.409235462217131	2.23596595965423	1	2	3	0	11	1	1	3
-Mir26a-2	-0.715034883511368	3.11546420527345	1.32372336809166	0.249924914221204	0.346493714612873	0.304126393558787	131	4.09235462217131	2.23596595965423	18.4315248043731	5.60127989245543	11.7988777185135	17.6336279365311	3.80785033348115	12.1818933873914	10	3	31	8	17	29	11	22
-Gm13375	-1.6921982855423	-1.49322451341955	1.31837615791593	0.250883687602521	0.347400834410773	0.549500512407157	5	0	0	0	0.553722426699609	0	0.74532198655141	1.1891306325402	0.700159986556928	0	0	0	1	0	1	2	1
-Yaf2	-1.67782445744683	-0.487813039725939	1.31308001418568	0.251837758331466	0.347986900409276	1.17230049674363	10	0	0	0	1.10744485339922	0.818470924434263	0	3.56739189762061	0	0	0	0	2	2	0	6	0
-Rnf126	-1.6247427069646	-1.5483229499814	1.31264181313975	0.251916897228801	0.347986900409276	0.388474138185462	5	0.700159986556928	0	0	0	1.10744485339922	0.409235462217131	0.74532198655141	0	1	0	0	0	2	1	1	0
-Mir223	0.392453416059884	5.98833711727872	1.3035785418167	0.253560594977612	0.349555682071357	0.104178045605271	928	40.1050752972789	81.2400965341037	127.236977681802	65.1148787497943	82.5921440295944	62.6297819814725	18.3469152431364	76.9674173112457	98	109	214	93	119	103	53	139
-Snord8	-0.978027022403874	1.09887870775351	1.30298812584026	0.25366812862396	0.349555682071357	0.4314327128184	32	0.74532198655141	1.7836959488103	2.80063994622771	1.38810326100159	6.08056135742452	1.3846728485386	3.32233456019766	0.818470924434263	1	3	4	2	10	4	6	2
-F420014N23Rik	-1.372332867125	0.486804153233623	1.30132325747801	0.253971656824851	0.349555682071357	0.978195779320001	22	0	1.2161122714849	1.3846728485386	0	3.27388369773705	0	4.75652253016081	0	0	2	4	0	8	0	8	0
-F630028O10Rik	0.392450488800123	5.98834207543087	1.29739234247459	0.25469009215405	0.35012216282864	0.104716472119336	928	73.0415546820382	64.8076194734411	149.834237123183	64.5468016365737	72.3586801533518	35.6553258498689	29.3472886150793	56.8837292481813	98	109	214	93	119	103	53	139
-Mir1945	-1.60978084536385	-1.55009830160392	1.29570121271995	0.254999942083813	0.35012627426911	0.378858489230937	5	0	0.553722426699609	0	0	1.1891306325402	0	0.694051630500793	0.608056135742452	0	1	0	0	2	0	1	1
-Mir3082	0.661138784925018	2.97567078622387	1.29273748445739	0.255544079405897	0.350451676204481	0.24963376787416	112	9.12084203613678	4.1540185456158	13.2893382407906	6.5477673954741	7.4532198655141	7.72934911151132	7.70175985212621	7.63456793550872	15	12	24	16	10	13	11	11
-Klc2	-1.65680060376313	-1.51683877037243	1.27647893144847	0.258554746351741	0.354154820633057	0.529733958421577	5	0	0	0	0.594565316270102	0.700159986556928	1.38810326100159	0.608056135742452	0	0	0	0	1	1	2	1	0
-Rmi1	-1.45414479134642	-0.862825068790834	1.26709959878699	0.260311499173742	0.356039233357995	0.605978592018314	8	0.553722426699609	0	0.74532198655141	0	0.700159986556928	0	2.43222454296981	0.34616821213465	1	0	1	0	1	0	4	1
-Mir134	1.03495548835917	1.45319323033477	1.26580803072866	0.260554566042004	0.356039233357995	0.601898706633359	40	1.38810326100159	3.64833681445471	3.4616821213465	4.42977941359688	2.86464823551992	5.21725390585987	0	0	2	6	10	8	7	7	0	0
-C230037L18Rik	-1.62980533639894	-1.52772398832634	1.2624738205075	0.261183349066953	0.35647153263803	0.484879154690579	5	0	0.700159986556928	0	0	0.34616821213465	0	0.409235462217131	1.49064397310282	0	1	0	0	1	0	1	2
-Mir3060	1.08677713577326	0.277864369948646	1.25611314182789	0.262388104130247	0.357668836230783	0.473324331323197	19	0.34616821213465	0.553722426699609	3.27388369773705	2.23596595965423	1.7836959488103	0.700159986556928	0	1.2161122714849	1	1	8	3	3	1	0	2
-4930562F07Rik	-1.64522099748687	-0.476339007188187	1.25291626650739	0.262996216290631	0.357668836230783	1.1878443646274	10	0	0.818470924434263	0	0	1.40031997311386	0	3.64833681445471	0	0	2	0	0	2	0	6	0
-Mir299	0.843754595626436	1.52663929643581	1.25289109673179	0.263001011040865	0.357668836230783	0.353242653337154	43	4.85836141350555	3.04028067871226	4.1540185456158	1.66116728009883	2.86464823551992	2.98128794620564	1.1891306325402	2.10047995967078	7	5	12	3	7	4	2	3
-Myeov2	-1.69291253107605	-1.64496689941108	1.24473900338444	0.264559683155445	0.359360236286146	0.683475557730936	5	0	0	0.34616821213465	0	1.22770638665139	0	0.594565316270102	0	0	0	1	0	3	0	1	0
-Pvt1	-1.32096490868673	-0.847731465862789	1.23855062742672	0.265750566194178	0.360548627856786	0.35441856020169	8	0.553722426699609	0	0	0.594565316270102	1.40031997311386	0.694051630500793	1.2161122714849	0.34616821213465	1	0	0	1	2	1	2	1
-Snora44	-0.381633059781074	5.65314644811287	1.22201591534437	0.268965390360777	0.364170733203647	0.102330578596002	724	52.7479239180603	44.388097909199	28.0396251829066	32.1159007485773	65.0684384925239	61.1164028972156	63.6184888409009	61.6140788170097	76	73	81	58	159	82	107	88
-Mir16-1	-0.412537352408144	5.07566733928455	1.22153990110487	0.269058657397611	0.364170733203647	0.116318778939368	499	21.5951746412848	13.9140057153825	64.8430128299727	27.9445698646948	66.5151987229082	49.2776657655563	30.4028067871226	26.3087841222334	39	34	87	47	95	71	50	76
-Snord92	-0.710096609221731	2.83572908658428	1.2111718792087	0.271100158349136	0.36649914772081	0.316545752043228	106	6.30143987901235	3.47025815250396	10.3369543076217	2.7693456970772	12.735615814091	3.27388369773705	21.6143376099909	4.16195721389071	9	5	17	8	23	8	29	7
-Gm16973	-1.47669981296583	-1.00488414037259	1.16547208604198	0.280333561977	0.378533247592612	0.807783550728712	8	0	0	1.10744485339922	0	2.98128794620564	0	1.40031997311386	0	0	0	2	0	4	0	2	0
-Mir196b	1.25717008543347	-0.50306250554666	1.14571235013042	0.284448506905949	0.383635634018544	0.561933397726954	10	1.10744485339922	0	1.49064397310282	1.7836959488103	0	0.694051630500793	0	0.6923364242693	2	0	2	3	0	1	0	2
-2310040G24Rik	-1.45685241958596	-1.01497652446792	1.14394094950534	0.284821122578047	0.383684652729105	0.794086796420206	8	0	0	1.49064397310282	0	2.80063994622771	0	0	0.6923364242693	0	0	2	0	4	0	0	2
-Pafah1b1	-0.979759016418312	1.50245301128808	1.12270570223865	0.289336591381148	0.389307842884304	0.597146443197918	40	1.03850463640395	1.66116728009883	0.818470924434263	2.98128794620564	4.75652253016081	0	11.1048260880127	2.43222454296981	3	3	2	4	8	0	16	4
-E030003E18Rik	-1.37677029350632	-0.911606444076738	1.10868384048074	0.292368231420679	0.392923618434623	0.650179476705915	8	0	0	0.409235462217131	0.74532198655141	1.7836959488103	0	2.08215489150238	0	0	0	1	1	3	0	3	0
-Gm11696	-1.6474567394522	-1.48131673919125	1.08635659782644	0.297279881147042	0.399054522810324	0.900717839549015	5	0	0.700159986556928	0	0	0	0.553722426699609	0	2.23596595965423	0	1	0	0	0	1	0	3
-4930568G15Rik	-1.63434903676238	-1.50910322195022	1.07512093530211	0.299791605870636	0.401953257694942	0.88678752728023	5	0.34616821213465	0	0	0	0.594565316270102	0	2.08215489150238	0	1	0	0	0	1	0	3	0
-Snord35b	-1.11151028366679	0.0545541991626386	1.03680869845452	0.308564847475744	0.413230623204019	0.579271233846859	15	1.22770638665139	0.74532198655141	0	0	3.47025815250396	0.608056135742452	0.6923364242693	1.66116728009883	3	1	0	0	5	1	2	3
-Gt(ROSA)26Sor	1.01120227557646	0.983570556736739	1.03355528158596	0.309325094602678	0.413344830354892	0.651740514579554	26	1.22770638665139	6.70789787896269	0.594565316270102	2.10047995967078	2.08215489150238	0	1.3846728485386	1.66116728009883	3	9	1	3	3	0	4	3
-Wbscr25	1.57399341703069	-1.78130174790484	1.03334353864081	0.309374658302435	0.413344830354892	0.638146949527696	4	1.49064397310282	0.594565316270102	0	0	0	0	0.553722426699609	0	2	1	0	0	0	0	1	0
-Irf3	-1.5346761545771	-1.58329226164049	1.02731268498339	0.310790677441742	0.414751067790676	0.697639468549404	5	0.694051630500793	0	0	0	1.22770638665139	0	0.594565316270102	0	1	0	0	0	3	0	1	0
-Fam172a	-1.03402893186865	0.604002126955515	1.018576530994	0.312856898096335	0.417020701784951	0.636367573855024	23	0.594565316270102	0.700159986556928	2.08215489150238	1.2161122714849	2.7693456970772	0.553722426699609	2.86464823551992	0	1	1	3	2	8	1	7	0
-A630010A05Rik	0.949572488616649	0.718313836775746	1.00067217278155	0.317147916372748	0.421790112728613	0.536546495626548	24	1.49064397310282	3.56739189762061	3.50079993278464	1.38810326100159	3.04028067871226	0.34616821213465	0	1.22770638665139	2	6	5	2	5	1	0	3
-2610027K06Rik	-1.27624242575249	-0.359242963660928	0.999807031473748	0.31735720510257	0.421790112728613	0.831448038206786	11	0	1.1891306325402	0.700159986556928	0	0.608056135742452	0	3.32233456019766	0.409235462217131	0	2	1	0	1	0	6	1
-Mrpl48	-1.11768365627351	-0.384442829883447	0.999035494819305	0.317544002483679	0.421790112728613	0.464594138402513	11	1.40031997311386	0.694051630500793	0	0	1.66116728009883	0.409235462217131	0.74532198655141	1.7836959488103	2	1	0	0	3	1	1	3
-Chkb	-0.980518104316082	0.868956035555252	0.988376398728009	0.320139520836939	0.424490647681999	0.616914850952162	28	1.49064397310282	1.1891306325402	1.40031997311386	1.38810326100159	8.51278590039432	0.6923364242693	2.21488970679844	0	2	2	2	2	14	2	4	0
-B630019K06Rik	-1.29011544235618	-1.11663074558135	0.987634695173225	0.320321163588257	0.424490647681999	0.543899136641392	7	0	0	1.2161122714849	0	0.553722426699609	0	1.49064397310282	1.1891306325402	0	0	2	0	1	0	2	2
-Mir25	-0.307341631802256	10.3901562647106	0.978979592374074	0.322450858265771	0.426817203342511	0.0921044561482298	19593	629.333809660793	783.517233779947	1435.5980014577	1349.03279565805	1755.75137894561	1426.22589261646	2371.57442142121	1602.22791768136	1818	1415	3508	1810	2953	2037	3417	2635
-Snord98	-0.405906224465692	5.17577368514848	0.966419614738753	0.325574742787118	0.430452817520395	0.148055095733361	553	24.3637867747828	9.82165109321115	111.798297982712	19.0260901206433	51.8118390052127	53.4419755485611	58.3733890312754	19.3854198795404	44	24	150	32	74	77	96	56
-1600002D24Rik	1.27011387184163	-1.04585152517957	0.961158554000621	0.326895153468287	0.431587161501975	0.571178325056528	7	0	0.694051630500793	1.2161122714849	0.6923364242693	0	0	1.49064397310282	0	0	1	2	2	0	0	2	0
-Map1lc3a	-1.14709638433051	0.508393686785022	0.959990722198208	0.32718921533673	0.431587161501975	0.906355460018944	21	0.74532198655141	0	1.40031997311386	2.08215489150238	3.64833681445471	0	4.98350184029649	0	1	0	2	3	6	0	9	0
-8430429K09Rik	-1.3414156662313	-0.646531504052733	0.95101637800707	0.329460721920131	0.434081620913244	1.09628514397537	11	0	0	1.03850463640395	0	2.86464823551992	0	0.594565316270102	0	0	0	3	0	7	0	1	0
-Mir505	-0.943456398194506	0.15617379176166	0.947097472025823	0.330459212871538	0.434894996408795	0.393870389120889	16	1.38810326100159	0.608056135742452	0.34616821213465	0.553722426699609	1.22770638665139	1.49064397310282	1.1891306325402	2.80063994622771	2	1	1	1	3	2	2	4
-2210015D19Rik	-1.68603662544734	-1.44669874969517	0.944398994380489	0.331149094714323	0.435300826116408	1.44754483144648	5	0.74532198655141	0	0	0	0	0	2.21488970679844	0	1	0	0	0	0	0	4	0
-Gm9776	-1.40607274664126	-1.117570120137	0.909181557848226	0.340331668786721	0.446856656024912	1.04170396479238	7	0	0	1.2161122714849	0	0.553722426699609	1.63694184886853	0	0	0	0	2	0	1	4	0	0
-Gm10336	1.46642692596801	-1.85743790875601	0.903427148882018	0.341864425738265	0.447838472752423	0.638146949527696	4	0	0	0.700159986556928	1.38810326100159	0	0	0	0.409235462217131	0	0	1	2	0	0	0	1
-Gm16897	1.46642692596801	-1.85743790875601	0.903427148882018	0.341864425738265	0.447838472752423	0.638146949527696	4	0	0	0.608056135742452	0.6923364242693	0	0	0	0.594565316270102	0	0	1	2	0	0	0	1
-Mir32	-0.44118887598408	4.19350189789183	0.898649650574614	0.343144047653345	0.448620773316011	0.176547126031611	274	10.5207261072926	5.32006100882271	40.9927092603276	16.6478288555628	33.6076793547326	24.9858586980285	17.6336279365311	15.9237377581939	19	13	55	28	48	36	29	46
-4930474G06Rik	1.46102259696366	-1.84717448236549	0.896800174910108	0.343641153267479	0.448620773316011	0.638146949527696	4	0.409235462217131	0.74532198655141	0.594565316270102	0	0	0	0.34616821213465	0	1	1	1	0	0	0	1	0
-A430093F15Rik	1.46102259696366	-1.84717448236549	0.896800174910108	0.343641153267479	0.448620773316011	0.638146949527696	4	0.553722426699609	0.409235462217131	0.74532198655141	0	0	0	0.608056135742452	0	1	1	1	0	0	0	1	0
-Mir872	-0.31739399651627	5.84043746331986	0.886164346084638	0.346518854683679	0.451860586507517	0.0990643765497606	859	43.7800417734565	22.8471020008869	90.8104779787359	27.8280114307649	135.648601552357	73.7260992174926	45.5103991262003	81.8980923990936	72	66	164	68	182	124	65	118
-Fam19a2	1.4480882584731	-1.85004212492862	0.882418462846213	0.347540136529334	0.452674995182614	0.638146949527696	4	0.694051630500793	0	0.34616821213465	0.553722426699609	0	0.74532198655141	0	0	1	0	1	1	0	1	0	0
-Nol8	-1.14310540598069	-0.147512884347668	0.880430696423492	0.348083742288729	0.452866077481687	0.84067895002272	14	0	0	1.40031997311386	1.38810326100159	3.64833681445471	0	2.21488970679844	0	0	0	2	2	6	0	4	0
-Mir501	-0.507499478420336	4.85304180354494	0.872779448711603	0.350186987306599	0.455083545007779	0.260597386343111	395	37.699480416032	12.4620556368474	4.42977941359688	13.9140057153825	53.6631830317015	39.2413108738267	20.3046396101509	61.0765434840698	62	36	8	34	72	66	29	88
-Gm6225	-1.33737355871558	-0.76777742001415	0.847486445177161	0.357264384067252	0.463238955378804	1.06898496044319	8	0	0	0	1.38810326100159	0	1.03850463640395	0	1.22770638665139	0	0	0	2	0	3	0	3
-Srsf7	-1.31253914025462	-0.791928890076212	0.847450549508221	0.357274566812749	0.463238955378804	0.989656808613828	8	0.608056135742452	0	0	0.409235462217131	0.74532198655141	0	3.50079993278464	0	1	0	0	1	1	0	5	0
-Mir676	0.291337691824197	6.50357735691488	0.837065743660259	0.360237320273243	0.466550263827208	0.0910787939974285	1363	80.843474298143	40.9235462217131	271.297203104713	82.050013645274	131.630077472703	94.3910217481078	86.9520274111706	51.2328953959282	146	100	364	138	188	136	143	148
-Mir874	-0.386150307522115	4.9631232643235	0.831624548011229	0.361803194305119	0.468046989458209	0.152452898646276	439	26.7554392321546	32.2073593816187	27.0680135895309	26.1464138369254	26.654952334368	36.5456801621742	14.7324766398167	64.8430128299727	45	46	39	43	77	66	36	87
-A930016O22Rik	1.07570061925198	0.391593006351726	0.820471077529275	0.365042469843883	0.471702670545719	0.949523508015469	20	0	0	4.75652253016081	4.20095991934157	0	0	0.6923364242693	2.21488970679844	0	0	8	6	0	0	2	4
-Scarna10	-0.865381535729171	0.577010125134298	0.817565599060581	0.365892890193918	0.472266728180158	0.523746471452758	23	0	1.40031997311386	3.47025815250396	0.608056135742452	2.42317748494255	1.66116728009883	1.63694184886853	0.74532198655141	0	2	5	1	7	3	4	1
-Mir3058	1.11179527728488	-0.603337449604796	0.814544576184019	0.36678004734819	0.472876874603711	0.650796215220554	9	1.49064397310282	1.7836959488103	0.700159986556928	0	0	0	1.10744485339922	0.409235462217131	2	3	1	0	0	0	2	1
-Wiz	-0.857742297715704	0.701947808508795	0.810671238982327	0.367921873088047	0.473663971071304	0.553818080700373	26	0	0.74532198655141	3.56739189762061	1.40031997311386	6.94051630500793	0.608056135742452	1.03850463640395	1.66116728009883	0	1	6	2	10	1	3	3
-Mir879	0.812363402700543	0.334336689004371	0.809549677514561	0.368253422163819	0.473663971071304	0.37152081648582	19	2.23596595965423	0.594565316270102	4.20095991934157	1.38810326100159	1.82416840722736	0.34616821213465	1.10744485339922	0.409235462217131	3	1	6	2	3	1	2	1
-4930523C07Rik	-1.09211471521139	-1.02690937822298	0.808257447298417	0.368635938923153	0.473663971071304	0.348360020054753	7	0.608056135742452	0	0	0.409235462217131	0.74532198655141	0.594565316270102	1.40031997311386	0.694051630500793	1	0	0	1	1	1	2	1
-4921511C10Rik	-1.2256092071291	-1.03320326700344	0.805325970904239	0.369505747077211	0.473839841020977	0.735931643655989	7	0	0.694051630500793	0.608056135742452	0	0	0	2.23596595965423	1.1891306325402	0	1	1	0	0	0	3	2
-Oaz1-ps	-0.737820867576816	1.58263227399166	0.804997517356526	0.369603381690333	0.473839841020977	0.4438156606492	41	1.2161122714849	2.0770092728079	1.10744485339922	1.63694184886853	3.72660993275705	6.54021847897112	4.9011199058985	2.77620652200317	2	6	2	4	5	11	7	4
-1700012D01Rik	-1.0859821547572	-1.024039731605	0.798006856830892	0.371689955439951	0.475456289922543	0.351068946209794	7	0.409235462217131	0.74532198655141	0	0	0.694051630500793	0.608056135742452	0.6923364242693	0.553722426699609	1	1	0	0	1	1	2	1
-4933400L20Rik	-1.39384902482183	-1.91033091593125	0.79798120266498	0.371697642954346	0.475456289922543	0.638146949527696	4	0	0	0.700159986556928	0	0.608056135742452	0.34616821213465	0.553722426699609	0	0	0	1	0	1	1	1	0
-5430417L22Rik	-1.39057474572072	-1.91218771891614	0.794543710086224	0.372729733882185	0.476242582709489	0.638146949527696	4	0	0	0.694051630500793	0	0.34616821213465	0	0.818470924434263	0	0	0	1	0	1	0	2	0
-Rit1	-1.18066685446434	-0.884962013744858	0.791583104599352	0.373621858343823	0.476818313576534	0.720336278635795	8	0.594565316270102	0.700159986556928	0	0	1.3846728485386	0	0.818470924434263	0	1	1	0	0	4	0	2	0
-Mipep	-1.08044068436668	-0.0515533594384622	0.787886801050346	0.374739876264079	0.476818313576534	0.841794812461123	14	0.553722426699609	0.818470924434263	0.74532198655141	0	2.80063994622771	0	3.64833681445471	0	1	2	1	0	4	0	6	0
-4933433G15Rik	1.36260750472985	-1.9178801928314	0.787517262160391	0.374851908219239	0.476818313576534	0.638146949527696	4	0	0.608056135742452	0.6923364242693	0	0	0	0	0.700159986556928	0	1	2	0	0	0	0	1
-Mir487b	1.36260750472985	-1.9178801928314	0.787517262160391	0.374851908219239	0.476818313576534	0.638146949527696	4	0	0.74532198655141	1.1891306325402	0	0	0	0	0.553722426699609	0	1	2	0	0	0	0	1
-Mir434	0.398704294242934	5.32809134795326	0.783610869712371	0.376039077482178	0.477795754350964	0.18096155087466	623	49.1912511123931	33.2956577111257	112.725757835665	38.8668913080444	98.5050939902772	22.5009337887522	7.19839154709492	18.0063603375538	66	56	161	56	162	65	13	44
-Sh2d3c	0.900515173139309	-0.101480748012929	0.763563114755328	0.38221575013348	0.485103638378532	0.444798572471769	13	1.38810326100159	1.82416840722736	0.34616821213465	1.10744485339922	0.818470924434263	0	1.1891306325402	0.700159986556928	2	3	1	2	2	0	2	1
-Ppargc1a	-0.952606212022499	0.293782672785089	0.75838732080199	0.383833678116596	0.486615807478929	0.702746747997422	18	0.553722426699609	0.818470924434263	2.23596595965423	0	2.10047995967078	0	4.86444908593961	0.34616821213465	1	2	3	0	3	0	8	1
-4930426L09Rik	-1.33608764035918	-1.94442030790985	0.737239117955896	0.390546724942404	0.494576929144598	0.638146949527696	4	0	0	0.594565316270102	0	1.38810326100159	0.608056135742452	0	0	0	0	1	0	2	1	0	0
-Mir130a	-0.261350701998935	9.55082938449014	0.734046919676931	0.391574561217655	0.495328796396169	0.0885182047386422	11048	739.368945804116	579.533111468162	1201.51892422708	340.97568895263	1090.27945817153	599.12071668588	822.835473152757	986.383859692098	1056	835	1976	985	1969	1464	1104	1659
-Vaultrc5	0.282392631962779	7.14209168134461	0.729952648369178	0.392898537427318	0.496274575782948	0.10070095996879	2022	156.878483021553	55.7330821536786	212.07568942595	110.493574798625	181.113242731993	94.5358852869461	183.441916477915	198.498766323227	258	161	383	270	243	159	262	286
-5031425E22Rik	-0.655319614563334	1.53769192518981	0.729047433685358	0.393192126650118	0.496274575782948	0.363571080538495	41	2.98128794620564	1.7836959488103	2.80063994622771	2.77620652200317	3.04028067871226	1.73084106067325	4.98350184029649	2.86464823551992	4	3	4	4	5	5	9	7
-Scarna9	-0.599527727601071	2.21560927778464	0.724004344056638	0.394833544677201	0.497420367765052	0.348222237256779	67	5.94565316270102	3.50079993278464	2.08215489150238	3.04028067871226	7.26953245482764	3.87605698689727	3.27388369773705	5.96257589241128	10	5	3	5	21	7	8	8
-BB123696	-1.32246101499089	-1.95221127258358	0.723580867527716	0.394971825762609	0.497420367765052	0.638146949527696	4	0	0	0.553722426699609	0	1.49064397310282	0	0	0.694051630500793	0	0	1	0	2	0	0	1
-Prmt1	-1.06380483859566	-0.662947500131192	0.721243512173664	0.395736317328835	0.497833669318854	0.738498350667854	10	0.700159986556928	0	1.2161122714849	0	2.76861213349805	0	1.49064397310282	0	1	0	2	0	5	0	2	0
-Gm10649	1.12566344203322	-1.18821756557948	0.712277825904559	0.398688664467222	0.500995337177424	0.562352672840447	6	1.1891306325402	0.700159986556928	0	0.608056135742452	0	0	0.409235462217131	0.74532198655141	2	1	0	1	0	0	1	1
-Neat1	-0.639359274050819	2.1571676262454	0.709321034654789	0.399669304108483	0.501675111097667	0.419913557357179	65	2.04617731108566	5.21725390585987	2.37826126508041	4.20095991934157	14.5750842405167	0.608056135742452	4.8463549698851	3.87605698689727	5	7	4	6	21	1	14	7
-9530082P21Rik	-1.29928622234974	-1.81190568253906	0.70061364459267	0.402577577574511	0.504216263460502	0.638146949527696	4	0	0	0	0.700159986556928	0	0	1.03850463640395	0	0	0	0	1	0	0	3	0
-Mir1196	-1.29928622234974	-1.81190568253906	0.70061364459267	0.402577577574511	0.504216263460502	0.638146949527696	4	0	0	0	0.700159986556928	0	0	1.03850463640395	0	0	0	0	1	0	0	3	0
-Fendrr	-1.29192105353688	-1.81623114353469	0.693296919413	0.405045235000079	0.506665978812924	0.638146949527696	4	0	0	0	0.700159986556928	0	0.608056135742452	0.34616821213465	0.553722426699609	0	0	0	1	0	1	1	1
-Scarna8	-0.999506227456247	-0.699029941590388	0.690854219790067	0.405873980809458	0.506665978812924	0.557509606131874	9	0	0.34616821213465	1.10744485339922	0	0	1.1891306325402	0.700159986556928	2.08215489150238	0	1	2	0	0	2	1	3
-Mir466d	-1.28861313716212	-1.81815026371424	0.690049238262354	0.40614763346158	0.506665978812924	0.638146949527696	4	0	0	0	0.694051630500793	0	0	1.10744485339922	0.409235462217131	0	0	0	1	0	0	2	1
-Mir4660	-0.865223107806529	0.870609125534787	0.689572866769698	0.406309702553747	0.506665978812924	0.719121791949277	26	0.694051630500793	1.82416840722736	0.34616821213465	1.66116728009883	2.86464823551992	0	5.94565316270102	0.700159986556928	1	3	1	3	7	0	10	1
-Nup88	-0.994879007728008	-2.30163521641929e-05	0.686180066902962	0.407466728609021	0.50755408006866	0.863762527575565	15	0.409235462217131	0.74532198655141	1.7836959488103	0	2.08215489150238	0	2.42317748494255	0	1	1	3	0	3	0	7	0
-E530011L22Rik	-1.27580227426471	-1.97993258785952	0.676913088521708	0.410651721914084	0.510963592915997	0.638146949527696	4	0	0	0.409235462217131	0	1.7836959488103	0	0	0	0	0	1	0	3	0	0	0
-Mir5100	-0.788526318434271	0.26769200133922	0.673888040189019	0.411699334582027	0.511709085793129	0.439360569117057	18	0.74532198655141	0.594565316270102	1.40031997311386	1.38810326100159	3.64833681445471	0.34616821213465	0.553722426699609	1.63694184886853	1	1	2	2	6	1	1	4
-Rmrp	-0.270601531427536	7.71631176697529	0.665425199542606	0.414651152181091	0.514817154122551	0.102898722153222	3178	192.94635327922	116.746778062551	235.048216039427	150.612500062294	245.950512792496	336.885537921237	130.804369579422	338.877433493553	278	192	679	272	601	452	220	484
-Rprl3	-1.10737514257782	-0.9227689236246	0.663773467279277	0.415230919844423	0.514976608198355	0.819188029544533	8	0.34616821213465	0.553722426699609	0	0	2.97282658135051	0	0	0.608056135742452	1	1	0	0	5	0	0	1
-Mir425	-0.277277075283714	6.71769389412303	0.662052099799532	0.415836408382323	0.5151675808515	0.106025700821499	1583	84.5198028682008	38.4246715469461	178.852343823974	51.9729037015757	229.559171857834	139.128284007204	66.5151987229082	170.736701103195	139	111	323	127	308	234	95	246
-Mir30c-2	-0.270730891354565	6.46238538348622	0.658397300723195	0.417126327191569	0.516205140266356	0.100489664927346	1345	64.2318014971547	36.0127206751076	248.19222152162	48.1597906178782	156.835836988752	96.4731766396102	119.179002605521	58.1562596386212	116	88	333	81	224	139	196	168
-Mir296	0.918650575247036	-0.460583863860555	0.646016707018832	0.421540421088128	0.521102514042853	0.586540297557589	11	0.700159986556928	0	1.82416840722736	1.03850463640395	1.66116728009883	0	0.74532198655141	0	1	0	3	3	3	0	1	0
-3110056K07Rik	-0.989603596520668	-0.711642114345864	0.64170435401604	0.423094298970678	0.522457354031973	0.638378811182629	9	0	0.34616821213465	1.10744485339922	0	0.74532198655141	0.594565316270102	2.80063994622771	0	0	1	2	0	1	1	4	0
-Scarna2	-0.755500412836096	1.01246755651737	0.637707615191119	0.424542123954873	0.523678446954065	0.605284868865558	32	1.49064397310282	0	5.60127989245543	1.38810326100159	5.47250522168207	0	3.32233456019766	2.04617731108566	2	0	8	2	9	0	6	5
-2610307P16Rik	1.19203527185237	-1.14177901756194	0.633147249903327	0.426203226686721	0.524736006102895	1.06155235506615	6	0	0.6923364242693	0	0.818470924434263	0	0	0	1.38810326100159	0	2	0	2	0	0	0	2
-Rtel1	-1.23039465340402	-1.84226267531762	0.632829687724376	0.426319261750555	0.524736006102895	0.638146949527696	4	0	0.74532198655141	0	0	0.694051630500793	0	0.6923364242693	0	0	1	0	0	1	0	2	0
-Ngrn	-1.22311681059493	-1.84654729525618	0.626012370899972	0.428821786317683	0.527230931392738	0.638146949527696	4	0	0.34616821213465	0	0	0.74532198655141	0.594565316270102	0	0.694051630500793	0	1	0	0	1	1	0	1
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-Gm12216	-0.918093834439149	-0.0491479794613772	0.610640381738943	0.434546796950864	0.532414737396833	0.753343264977246	14	0.6923364242693	1.10744485339922	0	0	2.97282658135051	0.700159986556928	0	2.43222454296981	2	2	0	0	5	1	0	4
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-Gm3086	-1.18327186593906	-1.88179103879875	0.58895609237948	0.442823075448616	0.540914268480127	0.638146949527696	4	0	0	0	0.409235462217131	1.49064397310282	0	0.700159986556928	0	0	0	0	1	2	0	1	0
-Ube2w	-0.802279929921059	-0.272312900376418	0.587283890198468	0.443471347669765	0.540914268480127	0.410066216185432	12	0.74532198655141	1.1891306325402	0.700159986556928	0	1.82416840722736	0.34616821213465	1.66116728009883	0.409235462217131	1	2	1	0	3	1	3	1
-1700034H15Rik	-1.04674949572586	-0.982650907487663	0.586722593488428	0.443689277257317	0.540914268480127	0.758623085525841	7	0	1.1891306325402	0	0	0.608056135742452	1.03850463640395	0.553722426699609	0	0	2	0	0	1	3	1	0
-Mir15b	0.24656896070166	6.17618442670063	0.586618149871978	0.443729846886414	0.540914268480127	0.0916084466421848	1064	71.9424032686823	67.915518696022	160.325926645683	67.4942310674121	56.4254185779479	55.9259650966606	35.6034852128904	114.034263942366	121	97	231	111	163	101	87	153
-4921513I03Rik	1.14837184321152	-1.11988704450467	0.583826690283896	0.444816277422034	0.541659949347428	1.08155044855555	6	0	1.49064397310282	0	1.40031997311386	0	1.2161122714849	0	0	0	2	0	2	0	2	0	0
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-4930467D21Rik	-1.17267992160388	-1.87708901455605	0.579180146144083	0.446633856999225	0.542714835821209	0.638146949527696	4	0	0.594565316270102	0	0	1.2161122714849	0	0.553722426699609	0	0	1	0	0	2	0	1	0
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-Ccdc77	-1.0232112784976	-1.02595188621268	0.572008178023575	0.449462021652889	0.54499061286498	0.723536484205456	7	0.34616821213465	0	0	0.74532198655141	1.1891306325402	2.10047995967078	0	0	1	0	0	1	2	3	0	0
-6720483E21Rik	-0.825665353842278	-0.259023801546772	0.567288130543039	0.451338557855409	0.546685026022316	0.515159283405282	12	1.10744485339922	0.409235462217131	0.74532198655141	0	1.40031997311386	2.08215489150238	0	1.03850463640395	2	1	1	0	2	3	0	3
-Snord1b	-0.621761342358914	1.29867852621228	0.563020527811128	0.453045779725115	0.548170980558172	0.434159021715519	37	1.22770638665139	2.98128794620564	2.37826126508041	1.40031997311386	9.7167228270111	1.2161122714849	1.73084106067325	1.66116728009883	3	4	4	2	14	2	5	3
-Mir381	0.368492171592626	4.09543871906321	0.558832253931007	0.454731128164601	0.549627348766748	0.201394355653873	263	16.6478288555628	18.9043196370371	49.2776657655563	10.9450104433641	20.770092728079	11.0744485339922	9.82165109321115	11.1798297982712	28	27	71	18	60	20	24	15
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-Mir374	-0.335211309931185	4.48758817669401	0.546047559260372	0.459937171615764	0.554744516716265	0.171104819176038	323	17.0255718007886	9.34654172763554	17.7191176543875	17.1878894131195	56.6444709779072	19.0260901206433	25.9059195026063	34.0085298945389	28	27	32	42	76	32	37	49
-Snord110	-0.236098840513442	7.44069978615917	0.543138898139393	0.461134768678221	0.555601658988226	0.0950757338497175	2471	92.0807444278168	125.141268434112	121.542932278488	195.274360476469	263.392435107655	236.654075456242	184.617733713211	226.804938631935	266	226	297	262	443	338	266	373
-1110002L01Rik	-1.12773231903873	-1.9168419916144	0.539480899124843	0.462647938316189	0.556836811834147	0.638146949527696	4	0.74532198655141	0	0	0	1.82416840722736	0	0	0	1	0	0	0	3	0	0	0
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-Orc4	-0.889232103497828	-0.667483328457936	0.507621915776015	0.476170126587911	0.571301675492363	0.680577549026061	9	1.1891306325402	0	0.694051630500793	0	0.34616821213465	0.553722426699609	1.63694184886853	0	2	0	1	0	1	1	4	0
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-Mir500	0.514812662928076	1.62952105886076	0.451946124136276	0.501412217023574	0.59844282387437	0.39320640905673	47	2.04617731108566	2.98128794620564	7.72934911151132	3.50079993278464	6.94051630500793	4.25639295019716	0.34616821213465	1.10744485339922	5	4	13	5	10	7	1	2
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-5930430L01Rik	-0.730088886708952	0.446296889470283	0.334333961479016	0.563118170090904	0.658317450895207	1.11562132780517	18	0	1.38810326100159	0	1.3846728485386	0	0	4.47193191930846	3.56739189762061	0	2	0	4	0	0	6	6
-1700012D14Rik	-0.642764433929117	-0.105757332812396	0.332943645810879	0.56393088224827	0.65859277036364	0.690060012834436	15	0	0	2.76861213349805	0.409235462217131	3.72660993275705	1.1891306325402	1.40031997311386	0	0	0	5	1	5	2	2	0
-E130102H24Rik	-0.181549438835569	10.3401804295945	0.326501797576952	0.56772625333123	0.662347295553101	0.0965067785199278	19702	1024.33406033279	958.485301721595	3025.0792753187	539.330074505784	1691.62201356731	844.661994016159	2249.38175541216	1300.90891199898	1463	1381	4975	1558	3055	2064	3018	2188
-E130307A14Rik	0.672561998437389	-0.899707549812139	0.324527272235918	0.568899538624949	0.663038175251345	0.474102791309215	8	0	0.74532198655141	1.7836959488103	0.700159986556928	0	0	0.34616821213465	1.10744485339922	0	1	3	1	0	0	1	2
-Mir101a	-0.181804203945389	10.3393802641415	0.322678297680454	0.570002514408693	0.663645784632978	0.0979305840479287	19692	1088.17010036506	821.09470176901	3482.59577313416	1080.63838868973	1856.39538242171	714.491189845917	1669.47311649932	895.407191331083	1460	1381	4974	1557	3053	2064	3015	2188
-Mir219-1	-0.361737007917808	2.54971603536105	0.31804655678911	0.572783964405732	0.666204386734904	0.303377381844108	90	4.16430978300476	2.43222454296981	7.26953245482764	4.42977941359688	8.18470924434263	7.4532198655141	4.16195721389071	9.802239811797	6	4	21	8	20	10	7	14
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-Mirlet7g	-0.190117170453271	11.2463170342993	0.308903572919803	0.578353777357827	0.671313997930093	0.112129757403857	38152	1641.00027290548	1640.47484850288	7279.21350069232	1548.71897773602	2617.37785195009	2622.42941284935	1092.65868411974	3761.64006612497	2760	2343	10488	2547	7561	4736	2670	5047
-A330093E20Rik	-0.675263869419669	-0.668838437168626	0.306147904235998	0.580053661464462	0.672602873710316	0.636159736493662	9	0.608056135742452	0.34616821213465	0	0.409235462217131	2.23596595965423	0	2.10047995967078	0	1	1	0	1	3	0	3	0
-Gm14005	0.551706913406605	0.870438438938928	0.285764730765445	0.592947462091344	0.686350936905082	0.734749060352456	26	4.20095991934157	2.08215489150238	3.04028067871226	0.34616821213465	1.66116728009883	0	5.96257589241128	0	6	3	5	1	3	0	8	0
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-Mir5113	-0.577134361008808	-0.876744391070353	0.258750062173541	0.610980182020199	0.70275039081154	0.345492016177573	8	0.409235462217131	0	0.594565316270102	0.700159986556928	1.38810326100159	0	0.6923364242693	0.553722426699609	1	0	1	1	2	0	2	1
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-9330020H09Rik	-0.637644233323968	-1.2948908997764	0.219196758007953	0.639652631144922	0.719363988392913	0.696962843736185	6	0.608056135742452	0	0	0.409235462217131	2.23596595965423	0	0.700159986556928	0	1	0	0	1	3	0	1	0
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-Gm10033	-0.62501288129082	-0.783613695123238	0.21663388842083	0.641616783431397	0.719988789842337	1.03598349010569	10	0	0	2.21488970679844	0	3.72660993275705	0	0.700159986556928	0	0	0	4	0	5	0	1	0
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-Gm11747	-0.441154583804285	-0.316218521703034	0.195167907284729	0.658649773120057	0.736062087296753	0.336170657987361	12	0.553722426699609	0.409235462217131	2.23596595965423	0	1.40031997311386	0.694051630500793	1.2161122714849	0.6923364242693	1	1	3	0	2	1	2	2
-Cdh23	-0.452270902928101	-0.109703011953558	0.193990040275081	0.659616283784396	0.73642091956751	0.475027167675216	14	0	0	2.77620652200317	1.2161122714849	0.6923364242693	1.10744485339922	1.22770638665139	0.74532198655141	0	0	4	2	2	2	3	1
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-AA465934	-0.195968497271681	-0.0963017433158353	0.0241121145044687	0.876599982727317	0.923563103838017	1.11283572179254	15	0.608056135742452	0	1.10744485339922	1.22770638665139	6.70789787896269	0	0	0	1	0	2	3	9	0	0	0
-Snord7	-0.197744508631868	-0.639035159991515	0.0241058099091518	0.876615987253788	0.923563103838017	0.967351112788188	10	0.409235462217131	0	0.594565316270102	1.40031997311386	4.16430978300476	0	0	0	1	0	1	2	6	0	0	0
-Abhd10	0.198072683422052	-1.24024741782945	0.0236281257641893	0.877834907095501	0.923994122690007	0.404633715340202	6	0.74532198655141	0.594565316270102	0	0.694051630500793	0.608056135742452	0	0.553722426699609	0.409235462217131	1	1	0	1	1	0	1	1
-Mir3473	0.196161852261303	-1.23882474353175	0.0231628143337455	0.879034442556119	0.924010611020748	0.406741736841495	6	0.700159986556928	0.694051630500793	0	0.34616821213465	0.553722426699609	0.409235462217131	0	0.594565316270102	1	1	0	1	1	1	0	1
-6330549D23Rik	-0.162094669655219	-0.68954702630399	0.0229949435772117	0.879470222233596	0.924010611020748	0.337791910405273	9	0.409235462217131	0.74532198655141	0.594565316270102	0.700159986556928	1.38810326100159	1.2161122714849	0	0.553722426699609	1	1	1	1	2	2	0	1
-Adarb1	-0.160961548326802	-0.123013714846092	0.0211799322182982	0.884289850944861	0.927264157820721	0.692544806766039	14	1.2161122714849	0	1.10744485339922	0.818470924434263	4.47193191930846	0	1.40031997311386	0	2	0	2	2	6	0	2	0
-Gm10433	0.225832212990213	-1.83578916176503	0.0209644531097322	0.884875835328919	0.927264157820721	0.638146949527696	4	0.34616821213465	0.553722426699609	0	0	0.594565316270102	0	0	0.608056135742452	1	1	0	0	1	0	0	1
-Svip	0.225653243267786	-1.82407656689306	0.0209171196886713	0.885004967455535	0.927264157820721	0.638146949527696	4	0	1.38810326100159	0	0	0.553722426699609	0	0.74532198655141	0	0	2	0	0	1	0	1	0
-Mir187	0.0942769746488839	2.5273253807264	0.0197476055386647	0.888244273923545	0.929187947651877	0.335631890605114	82	2.7693456970772	3.32233456019766	5.72929647103984	9.68918582516833	5.94565316270102	13.3030397445816	3.47025815250396	4.25639295019716	8	6	14	13	10	19	5	7
-2610035D17Rik	0.215718872176664	-1.82888503952518	0.0191974462919147	0.889801924027029	0.929187947651877	0.638146949527696	4	0	0.553722426699609	0	0.74532198655141	0.594565316270102	0	0.694051630500793	0	0	1	0	1	1	0	1	0
-B230319C09Rik	0.214303069493782	-1.82957266025757	0.0189579419944019	0.89048712809598	0.929187947651877	0.638146949527696	4	0.553722426699609	0.409235462217131	0	0	0.700159986556928	0	0.608056135742452	0	1	1	0	0	1	0	1	0
-4930565N06Rik	0.159509655511957	-0.862850882597741	0.0188629036487473	0.890760247348387	0.929187947651877	0.391590681076766	8	0.74532198655141	0.594565316270102	0.700159986556928	0.694051630500793	1.2161122714849	0	1.10744485339922	0	1	1	1	1	2	0	2	0
-Mir5114	0.186397613455716	-1.3047501273248	0.0187757104468318	0.891011438659261	0.929187947651877	0.606970175156446	6	0	0.6923364242693	0.553722426699609	0	1.49064397310282	0	0	0.694051630500793	0	2	1	0	2	0	0	1
-A230020J21Rik	0.157586258788334	-0.868234001557016	0.0185283643764711	0.891727259140057	0.929187947651877	0.384151248976418	8	0.553722426699609	0	0.74532198655141	1.1891306325402	1.40031997311386	0.694051630500793	0	0.34616821213465	1	0	1	2	2	1	0	1
-Fut8	-0.14159898095711	-0.124343230051396	0.0171304848860476	0.895867484667575	0.932181208568498	0.568440841559561	13	0.694051630500793	1.2161122714849	0.6923364242693	0.553722426699609	0.409235462217131	0.74532198655141	2.97282658135051	0	1	2	2	1	1	1	5	0
-G730013B05Rik	-0.1444644504645	-0.11612786759881	0.0170094840462109	0.89623381752817	0.932181208568498	0.704600874847864	14	0.6923364242693	1.10744485339922	0.818470924434263	0	3.56739189762061	0	1.38810326100159	0	2	2	2	0	6	0	2	0
-Snord88a	-0.045356821387815	5.38319253786929	0.0148091922381681	0.903142137735534	0.938511092127727	0.119396323989129	589	41.025006822637	51.1116790186558	53.4419755485611	31.6189190586075	33.2321483649264	34.3307904553758	41.3327816839303	43.9739972065332	69	73	77	52	96	62	101	59
-2310010J17Rik	0.160593166241322	-0.712339318033024	0.0144685482300719	0.904257165472018	0.938814764152477	1.02238827412666	10	1.2161122714849	0	1.66116728009883	0	3.72660993275705	0	0	0	2	0	3	0	5	0	0	0
-Mirg	0.046466455780014	6.97315439829676	0.0133211776496633	0.908114283021421	0.941962179024946	0.151390994081439	1940	67.1146158036095	123.723449767534	246.150040935822	129.529597513032	392.139171232948	142.285135763734	22.5009337887522	81.3971967248426	164	166	414	185	565	234	65	147
-Gm16291	-0.128584309543259	0.0521366329795151	0.0129026047756327	0.909563105648682	0.942608086780333	0.76402219191087	14	2.23596595965423	1.1891306325402	0	0.694051630500793	1.2161122714849	0.34616821213465	2.76861213349805	0	3	2	0	1	2	1	5	0
-Gm19522	0.133128085740831	-0.829962591291576	0.0112267403629041	0.915617013803418	0.948020882712976	0.649769689162674	8	0	0.553722426699609	0.409235462217131	1.49064397310282	0.594565316270102	0	2.08215489150238	0	0	1	1	2	1	0	3	0
-Rhno1	0.159916601574934	-1.78865128034686	0.0107877052439775	0.917277372855387	0.948878950524022	0.638146949527696	4	0	1.49064397310282	0	0	0	0	0.6923364242693	0	0	2	0	0	0	0	2	0
-Mir16-2	0.0578872268985141	3.19480487022685	0.00999483968919579	0.920364812100843	0.949540533089302	0.261387449317382	133	12.4929293490143	6.68861749316697	9.00037351550089	6.0909466936957	6.95700285769123	13.4157957579254	5.35108784643091	16.1036796908094	18	11	26	11	17	18	9	23
-4930452A19Rik	0.149444137245449	-1.92879183038896	0.00940265408085583	0.922752375917069	0.949540533089302	0.638146949527696	4	0	0.409235462217131	0.74532198655141	0	1.40031997311386	0	0	0	0	1	1	0	2	0	0	0
-Mir20b	0.149444137245449	-1.92879183038896	0.00940265408085583	0.922752375917069	0.949540533089302	0.638146949527696	4	0	0.409235462217131	0.74532198655141	0	1.40031997311386	0	0	0	0	1	1	0	2	0	0	0
-Snora78	0.0952564242056809	0.541952701642771	0.00939621357845333	0.922778753676933	0.949540533089302	0.591155323319973	22	0.818470924434263	0	2.97282658135051	2.80063994622771	3.47025815250396	0	1.3846728485386	1.10744485339922	2	0	5	4	5	0	4	2
-Snhg9	0.0952572647592143	0.541935691926325	0.00938990918195604	0.922804582839966	0.949540533089302	0.591819195993488	22	1.49064397310282	0	3.50079993278464	2.77620652200317	3.04028067871226	0	2.21488970679844	0.818470924434263	2	0	5	4	5	0	4	2
-4930527F14Rik	0.148246679588332	-1.80273590622697	0.0093641708890102	0.922910123747621	0.949540533089302	0.638146949527696	4	0	0	0	1.10744485339922	0	0.74532198655141	0	0.700159986556928	0	0	0	2	0	1	0	1
-A430071A18Rik	0.140089715305426	-1.79838759526887	0.00841358745094212	0.926916049667801	0.951945285932458	0.638146949527696	4	0	0	0	1.2161122714849	0	0	0.818470924434263	0	0	0	0	2	0	0	2	0
-Cd22	0.140089715305426	-1.79838759526887	0.00841358745094212	0.926916049667801	0.951945285932458	0.638146949527696	4	0	0	0	1.40031997311386	0	0	0.6923364242693	0	0	0	0	2	0	0	2	0
-Btbd19	0.13139826781368	-1.7952139152904	0.00745956192008634	0.931173283624132	0.955457478970444	0.638146949527696	4	0.74532198655141	0	0	0.694051630500793	0	0.6923364242693	0	0	1	0	0	1	0	2	0	0
-1810034E14Rik	-0.0582784540366963	2.09200681386011	0.00716964611245841	0.932520755264328	0.955980396906198	0.32866487607919	64	6.24646467450714	1.2161122714849	5.19252318201975	2.76861213349805	4.50159008438844	7.4532198655141	2.37826126508041	5.60127989245543	9	2	15	5	11	10	4	8
-Mir29b-1	0.105421115756166	-0.43157442729593	0.00687050063077876	0.933940211681206	0.956095747461183	0.877489638142529	10	0.34616821213465	1.66116728009883	0.409235462217131	0	0	2.80063994622771	0.694051630500793	0	1	3	1	0	0	4	1	0
-Zmynd8	-0.0719353339983849	1.09734258429151	0.00673343019890815	0.934601004243129	0.956095747461183	0.486960647190855	30	2.04617731108566	2.98128794620564	2.37826126508041	0.700159986556928	2.08215489150238	1.82416840722736	2.7693456970772	1.10744485339922	5	4	4	1	3	3	8	2
-Mir5129	0.0957314088382215	-0.822204343190538	0.00662119867327871	0.935147111451955	0.956095747461183	0.470649185108855	8	0	0.553722426699609	0.409235462217131	1.49064397310282	0	0.700159986556928	0.694051630500793	1.2161122714849	0	1	1	2	0	1	1	2
-Mdp1	0.103941610776393	-1.27776731451046	0.00594341709128976	0.938549115625586	0.958714897877165	0.655887599518928	6	0	0	0.608056135742452	0.6923364242693	0.553722426699609	0	1.49064397310282	0	0	0	1	2	1	0	2	0
-Thap6	0.0884668393261384	-0.897821946953951	0.00577369764406122	0.939431150174737	0.9587575512964	0.443269548229457	8	0	1.1891306325402	1.40031997311386	0	1.2161122714849	0.34616821213465	0.553722426699609	0	0	2	2	0	2	1	1	0
-Zfp821	-0.123537350109892	-1.92573779586961	0.00515432888996514	0.942766122414118	0.960815718152111	0.638146949527696	4	0	0	0.818470924434263	0	0	1.40031997311386	0	0	0	0	2	0	0	2	0	0
-Dio3os	-0.0783724880504645	-0.622642427168383	0.0050885292982894	0.943131993278145	0.960815718152111	0.510910213341106	9	0.694051630500793	1.2161122714849	0	0.553722426699609	0.409235462217131	0	1.1891306325402	1.40031997311386	1	2	0	1	1	0	2	2
-Gm4890	-0.116255852427914	-1.92943339707875	0.00453141926387435	0.946330285035873	0.963213965411179	0.638146949527696	4	0	0	1.40031997311386	0	0	0	1.10744485339922	0	0	0	2	0	0	0	2	0
-Mir147	0.096488117471615	-1.90056566943248	0.00412143444010482	0.94881225214317	0.964879482794436	0.638146949527696	4	0	0.74532198655141	0.594565316270102	0	0.694051630500793	0	0	0.553722426699609	0	1	1	0	1	0	0	1
-Mir3103	-0.108098888145008	-1.93359432954311	0.00387924299399423	0.950337012939027	0.965569485096554	0.638146949527696	4	0	0	1.10744485339922	0	0	0.594565316270102	0	0.694051630500793	0	0	2	0	0	1	0	1
-Lmf1	0.0679307624649559	-0.14337492663708	0.0034194404663257	0.953369493368774	0.967174636846159	0.635546740621643	13	0.700159986556928	2.08215489150238	0.608056135742452	0.34616821213465	2.21488970679844	0	2.23596595965423	0	1	3	1	1	4	0	3	0
-Gm10548	0.0609027211306225	-0.880709174563083	0.00330101054142751	0.954183212529461	0.967174636846159	0.252311230579068	8	0	0.34616821213465	1.10744485339922	0.409235462217131	0.74532198655141	0.594565316270102	0.700159986556928	0.694051630500793	0	1	2	1	1	1	1	1
-Gm15545	0.0849589739751836	-1.89448493270386	0.0032612312701028	0.954459808140908	0.967174636846159	0.638146949527696	4	0	0.594565316270102	0.700159986556928	0	0.608056135742452	0	0.553722426699609	0	0	1	1	0	1	0	1	0
-Plscr3	0.0814004336200907	-1.89261335490638	0.00301642056831319	0.956200644868514	0.968047332759487	0.638146949527696	4	0	0.74532198655141	0.594565316270102	0	0.694051630500793	0.608056135742452	0	0	0	1	1	0	1	1	0	0
-5430402O13Rik	-0.0927467442781055	-1.94142512096775	0.00279115036404498	0.957866291573585	0.968047332759487	0.638146949527696	4	0	0	1.2161122714849	0	0	0	0	1.1891306325402	0	0	2	0	0	0	0	2
-Gm6297	-0.0927467442781055	-1.94142512096775	0.00279115036404498	0.957866291573585	0.968047332759487	0.638146949527696	4	0	0	0.818470924434263	0	0	0	0	1.2161122714849	0	0	2	0	0	0	0	2
-Gm5095	0.0741497349563809	-1.89982855309554	0.00255353302993466	0.959698055373646	0.969040248833035	0.638146949527696	4	0.409235462217131	0	0.594565316270102	0	0.694051630500793	0	0.34616821213465	0	1	0	1	0	1	0	1	0
-Mir18	-0.0321144919271105	2.13829995459641	0.00222894649578897	0.96234448681064	0.970853279797471	0.319997109480565	62	4.9011199058985	4.85836141350555	4.86444908593961	2.42317748494255	3.87605698689727	3.68311915995418	2.98128794620564	7.72934911151132	7	7	8	7	7	9	4	13
-4930547E14Rik	0.0332717629837295	-1.87681159162927	0.000628960971966741	0.979991875252521	0.987622213297045	0.638146949527696	4	0	0	0.608056135742452	0.34616821213465	0	0	0	1.1891306325402	0	0	1	1	0	0	0	2
-Mir30a	-0.00674515544774862	15.2305157438047	0.000585365330948662	0.980697605315997	0.987622213297045	0.0746707420324099	565907	22165.4203400665	38322.2205825139	68810.8277478877	37443.855921078	63416.8855821185	38709.4616575002	22770.252657793	38928.9014866893	54163	51417	115733	53479	91372	63661	65778	70304
-2610002J02Rik	0.018998702253143	-1.31967503888113	0.000345631121349221	0.985167257251054	0.991248536616801	0.365725430522663	6	0	0	1.38810326100159	0.608056135742452	0.34616821213465	0.553722426699609	0.409235462217131	0	0	0	2	1	1	1	1	0
-Mir1306	0.010990964703492	0.387899924622603	0.000182949792714382	0.989208227531673	0.993710996805651	0.374307689020903	20	0.34616821213465	0.553722426699609	2.45541277330279	1.49064397310282	2.37826126508041	1.40031997311386	1.38810326100159	1.2161122714849	1	1	6	2	4	2	2	2
-2810001G20Rik	0.0139659525352028	-1.99687003375001	0.000177958964401981	0.989356435031744	0.993710996805651	0.638146949527696	4	0	0	1.40031997311386	0	1.2161122714849	0	0	0	0	0	2	0	2	0	0	0
-Snora31	-0.00608992937342303	4.51111691273084	0.000131880843156296	0.990837344181505	0.994323139587597	0.245986767999803	320	26.6060794891633	26.3739619590301	21.8900208867283	12.1158874247127	31.5621783218777	4.09235462217131	60.3710809106642	14.8641329067525	38	38	36	35	57	10	81	25
-2010320M18Rik	-0.0135816064033237	-0.577688977281378	9.37664770823687e-05	0.992273957831848	0.994889794276045	0.436705588816395	10	0	0	1.03850463640395	1.10744485339922	0.409235462217131	1.49064397310282	0.594565316270102	0.700159986556928	0	0	3	2	1	2	1	1
-2310001K24Rik	0.00612441798475525	-1.86264950933858	6.95515125732626e-05	0.993345915420738	0.995090157590046	0.638146949527696	4	0	0	0.594565316270102	0.700159986556928	0	0.608056135742452	0.34616821213465	0	0	0	1	1	0	1	1	0
-Mir1966	0.000918355090882732	-0.94191710317151	1.38947096530728e-05	0.997025843661245	0.997900427734632	0.449008936327196	8	0	0.34616821213465	1.66116728009883	0	1.49064397310282	0.594565316270102	0.700159986556928	0	0	1	3	0	2	1	1	0
-Mir376b	-0.00136357255892604	1.39148339025352	2.78221370209053e-06	0.998669131632702	0.998669131632702	0.592374698826143	42	1.49064397310282	2.37826126508041	7.70175985212621	2.08215489150238	9.72889817187923	1.73084106067325	0.553722426699609	0	2	4	11	3	16	5	1	0

--- a/rgedgeR/test-data/gentestdata.sh	Sat Jul 27 22:28:00 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-#!/bin/bash
-# generate test data for rgGSEA
-# ross lazarus June 2013 
-# adjust gseajar_path !
-GSEAJAR_PATH=/home/rlazarus/galaxy-central/tool_dependency_dir/gsea_jar/2.0.12/fubar/rg_gsea_test/8e291f464aa0/jars/gsea2-2.0.12.jar
-python ../rgGSEA.py --input_tab "gsea_test_DGE.xls"  --adjpvalcol "5" --signcol "2" --idcol "1" --outhtml "gseatestout.html" --input_name "gsea_test" --setMax "500" --setMin "15" --nPerm "10" --plotTop "20" --gsea_jar "$GSEAJAR_PATH" --output_dir "gseatestout" --mode "Max_probe" 
---title "GSEA test" --builtin_gmt "gseatestdata.gmt"
-
-

--- a/rgedgeR/test-data/test_bams2mx.xls	Sat Jul 27 22:28:00 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3243 +0,0 @@
-Contigname	11706Liv_CAAAAG_L003_R1_001_trimmed.fastq_bwa.sam.bam	11706He_AGTTCC_L001_R1_001_trimmed.fastq_bwa.sam.bam	11699He_GGCTAC_L001_R1_001_trimmed.fastq_bwa.sam.bam	11698He_TAGCTT_L001_R1_001_trimmed.fastq_bwa.sam.bam	11700Liv_ATTCCT_L003_R1_001_trimmed.fastq_bwa.sam.bam	11698Liv_ACTGAT_L003_R1_001_trimmed.fastq_bwa.sam.bam	11699Liv_ATGAGC_L003_R1_001_trimmed.fastq_bwa.sam.bam	11700He_CTTGTA_L001_R1_001_trimmed.fastq_bwa.sam.bam
-0610005C13Rik	40	0	2	0	6	70	6	2
-0610007N19Rik	10	17	11	42	2	6	6	10
-0610008F07Rik	16	0	0	0	8	5	4	1
-0610009B14Rik	0	0	0	1	0	0	0	0
-0610009L18Rik	3	2	2	11	0	1	1	1
-0610012G03Rik	6	0	0	0	4	5	2	0
-0610031O16Rik	33	0	0	0	10	25	10	0
-0610038B21Rik	0	0	0	2	0	0	0	0
-0610038L08Rik	0	0	0	0	0	3	0	0
-0610039K10Rik	9	0	0	1	3	1	4	3
-0610040B10Rik	0	0	0	0	0	0	2	0
-0610040F04Rik	2	1	0	1	2	5	2	0
-0610043K17Rik	9	2	0	4	4	12	0	1
-1110002L01Rik	3	1	0	0	0	0	0	0
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-1110017D15Rik	0	0	0	0	0	2	0	0
-1110019D14Rik	1	1	1	0	0	0	2	0
-1110020A21Rik	2	0	0	2	0	2	6	0
-1110028F11Rik	0	0	0	0	0	0	0	0
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-1110035M17Rik	0	0	0	0	0	0	0	1
-1110036E04Rik	0	0	0	0	0	0	0	0
-1110038B12Rik	9406	1346	1212	1600	7604	6486	8084	1328
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-1110054M08Rik	6	1	0	1	0	6	1	1
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-1500017E21Rik	4	1	3	0	0	7	1	4
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-Snhg10	4	1	0	0	0	2	3	0
-Snhg12	1273	233	180	1043	811	922	743	198
-Snhg3	28	9	2	10	6	18	18	3
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-Snhg6	390	145	138	191	236	256	215	191
-Snhg7	34	4	3	15	15	82	13	7
-Snhg8	42	7	5	14	36	19	33	8
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-Snora26	6	0	1	0	2	1	2	1
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-Snora2b	1	0	0	1	0	0	0	0
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-Snora30	0	0	0	0	0	0	0	1
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-Snora5c	0	0	0	0	0	0	0	0
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-Snord1a	62	7	9	27	54	32	31	8
-Snord1b	14	3	4	4	2	5	3	2
-Snord1c	0	0	0	0	0	0	0	0
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-Snord35b	5	3	1	0	1	2	3	0
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-Snord42a	61	93	100	30	31	20	35	68
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-Snord45c	323	57	49	190	212	322	212	62
-Snord47	120	5	8	29	31	49	25	10
-Snord49a	232	84	51	256	151	120	145	75
-Snord49b	393	62	57	216	245	123	294	95
-Snord4a	324	50	39	155	196	165	191	31
-Snord52	4584	654	591	753	3716	3171	3941	649
-Snord53	65	21	11	57	50	23	51	12
-Snord55	462	124	101	450	309	255	250	119
-Snord57	1737	785	744	2031	1351	1445	1388	787
-Snord58b	46	85	81	3	44	29	49	57
-Snord61	46	16	8	75	31	32	12	13
-Snord64	24	22	19	48	13	19	35	17
-Snord65	29	74	90	8	17	19	15	68
-Snord66	884	267	281	340	693	807	696	244
-Snord67	39	4	1	17	18	13	11	5
-Snord68	1644	460	353	1060	1295	805	1310	376
-Snord69	440	157	105	401	341	407	333	117
-Snord7	6	1	0	1	0	0	0	2
-Snord70	23	6	11	16	10	6	14	6
-Snord71	93	20	20	38	51	26	64	29
-Snord72	159	21	24	57	102	123	101	16
-Snord73a	29	3	3	7	6	9	2	5
-Snord8	10	1	3	4	4	6	2	2
-Snord82	47	17	14	19	19	40	18	17
-Snord83b	48	22	12	35	22	34	32	16
-Snord85	3804	911	737	1422	3047	1133	3156	882
-Snord87	390	145	138	190	235	255	215	191
-Snord88a	96	69	73	77	62	101	59	52
-Snord88c	74	29	22	35	41	65	52	23
-Snord89	13	2	2	3	2	8	3	3
-Snord90	43	2	3	46	14	48	10	5
-Snord91a	363	40	29	81	256	358	285	25
-Snord92	23	9	5	17	8	29	7	8
-Snord93	45	54	50	161	29	34	29	33
-Snord95	708	217	195	326	483	675	444	210
-Snord96a	145	16	22	56	71	106	59	12
-Snord98	74	44	24	150	77	96	56	32
-Snord99	931	126	80	847	655	668	555	108
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-Speer1-ps1	0	0	0	0	0	0	0	0
-Speer5-ps1	0	0	0	0	0	0	0	0
-Speer6-ps1	0	0	0	0	0	0	0	0
-Speer7-ps1	0	0	0	0	0	0	0	0
-Speer8-ps1	0	0	0	0	0	0	0	0
-Speer9-ps1	1	0	0	0	0	0	0	0
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-Sprr2g	0	0	0	0	0	0	0	0
-Sprr2j-ps	0	0	0	0	0	0	0	0
-Sqrdl	35	1	0	1	4	58	3	0
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-Srsf3	7	2	8	2	11	9	14	4
-Srsf7	1	1	0	0	0	5	0	1
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-St18	0	0	0	0	0	0	0	0
-St5	7	3	0	1	2	7	2	2
-St7l	8	1	1	1	3	12	4	2
-Stap2	10	0	2	2	1	6	4	0
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-Terc	22	1	0	0	18	10	15	0
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-Tk2	1	2	0	2	1	1	3	0
-Tmem161b	0	0	0	0	2	2	4	0
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-Tmem205	35	2	0	1	4	57	6	1
-Tmem41a	7	0	0	0	0	5	2	0
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-Trappc13	1	0	0	1	0	0	3	1
-Trim30e-ps1	0	0	0	0	0	0	0	0
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-Trmt61b	11	0	0	0	2	5	0	0
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-Vax2os	0	0	0	0	0	0	0	0
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-Vmn2r-ps11	0	0	0	1	0	0	0	0
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-Vmn2r-ps159	0	0	0	0	0	0	0	0
-Vmn2r-ps54	0	0	1	0	0	0	0	0
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-Vsig8	194	50	35	100	99	74	109	50
-Wac	15	0	0	0	2	15	2	2
-Wbscr25	0	2	1	0	0	1	0	0
-Wdr13	2	2	1	3	0	1	0	3
-Wdr73	4	0	0	0	0	2	1	0
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-Wls	1	1	0	3	2	0	0	1
-Wwp1	40	0	2	2	4	56	10	4
-Xist	0	0	0	0	0	8	0	0
-Yaf2	2	0	0	0	0	6	0	2
-Yars2	1	0	0	0	1	1	0	0
-Yipf2	1	0	0	1	0	10	0	0
-Ythdf3	16	4	1	4	3	19	3	2
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-Zc3h14	11	1	0	0	1	2	2	2
-Zc3h7a	336	148	60	20	17	99	14	60
-Zf12	0	0	0	0	0	0	0	0
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-Zfp133-ps	0	0	0	0	0	0	0	0
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-Zfp326	7	2	1	1	0	4	4	0
-Zfp389	0	0	0	0	0	0	0	0
-Zfp410	10	0	2	0	0	6	2	0
-Zfp414	1	0	0	0	0	4	0	0
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-Zfp572	0	0	0	0	0	0	0	0
-Zfp672	0	0	0	0	0	2	0	0
-Zfp783	0	0	0	0	0	0	0	0
-Zfp809	7	1	0	0	0	4	2	0
-Zfp821	0	0	0	2	2	0	0	0
-Zfp862	4	0	0	0	0	10	2	0
-Zim3	0	0	0	0	0	0	0	0
-Zmynd8	3	5	4	4	3	8	2	1
-Znf41-ps	0	0	0	0	0	0	0	0
-Zp4-ps	0	0	0	0	0	0	0	0
-Zscan4a	0	0	0	0	0	0	0	0
-Zxda	0	0	0	0	0	0	0	0

--- a/rgedgeR/tool_dependencies.xml	Sat Jul 27 22:28:00 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="r3" version="3.0.1">
-        <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
-    </package>package_ghostscript_9_07
-    <package name="ghostscript" version="9.07">
-        <repository changeset_revision="10222a7db54c" name="package_ghostscript_9_07" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
-    </package>
-    <package name="graphicsmagick" version="1.3.18">
-        <repository changeset_revision="50d546dfd6b9" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
-    </package>
-    <package name="biocbasics" version="2.12">
-        <install version="1.0"> 
-            <actions>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="6e89ec508745" name="package_r3" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu/">
-                        <package name="r3" version="3.0.1" />
-                    </repository>
-                </action>
-                <action type="make_directory">$INSTALL_DIR</action>
-                <action type="shell_command">echo "source('http://bioconductor.org/biocLite.R')" &gt; $INSTALL_DIR/runme.R</action>
-                <action type="shell_command">echo "installme=c('edgeR','limma','DESeq','DESeq2')" &gt;&gt; $INSTALL_DIR/runme.R</action>
-                <action type="shell_command">echo "biocLite()" &gt;&gt; $INSTALL_DIR/runme.R</action>
-                <action type="shell_command">echo "biocLite(installme)" &gt;&gt; $INSTALL_DIR/runme.R</action>
-                <action type="shell_command">echo "install.packages(c('stringr','gplots'),dependencies=T,repos='http://cran.us.r-project.org')" &gt;&gt; $INSTALL_DIR/runme.R</action>
-                <action type="shell_command">echo "quit(save='no')" &gt;&gt; $INSTALL_DIR/runme.R</action>                
-                <action type="shell_command"> export PATH=$PATH &amp;&amp; export R_HOME=$R_HOME &amp;&amp; export R_LIBS=$R_LIBS &amp;&amp; R CMD BATCH $INSTALL_DIR/runme.R </action>
-            </actions>
-        </install>
-        <readme>Installs some basic bioc packages for the edgeR wrapper and dependencies graphicsmagick (replaces imagemagick) and ghostscript for compressing R's bloated pdfs
-        It's clunky but this is the most convenient way I could get anything installed into the package_r3
-        Note we use cran at fred hutch since no fastest mirror thingy
-       </readme>
-    </package>
-</tool_dependency>