changeset 145:a240760dff72 draft

Uploaded
author iuc
date Tue, 28 Apr 2015 22:46:44 -0400
parents ab78085c7847
children 474c08e747b6
files rgToolFactory.py rgedgeRpaired_nocamera.xml test-data/edgeRtest1out.html test-data/edgeRtest1out.xls test-data/gentestdata.sh test-data/test_bams2mx.xls tool_dependencies.xml
diffstat 7 files changed, 0 insertions(+), 6787 deletions(-) [+]
line wrap: on
line diff
--- a/rgToolFactory.py	Fri Apr 10 22:46:53 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,638 +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
-#
-# march 2014
-# added ghostscript and graphicsmagick as dependencies 
-# fixed a wierd problem where gs was trying to use the new_files_path from universe (database/tmp) as ./database/tmp
-# errors ensued
-#
-# 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 = 'V001.1 March 2014' 
-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)
-        hlog = os.path.join(self.opts.output_dir,"compress_%s.txt" % os.path.basename(inpdf))
-        sto = open(hlog,'a')
-        our_env = os.environ.copy()
-        our_tmp = our_env.get('TMP',None)
-        if not our_tmp:
-            our_tmp = our_env.get('TEMP',None)
-        if not (our_tmp and os.path.exists(our_tmp)):
-            newtmp = os.path.join(self.opts.output_dir,'tmp')
-            try:
-                os.mkdir(newtmp)
-            except:
-                sto.write('## WARNING - cannot make %s - it may exist or permissions need fixing\n' % newtmp)
-            our_env['TEMP'] = newtmp
-            if not self.temp_warned:
-               sto.write('## WARNING - no $TMP or $TEMP!!! Please fix - using %s temporarily\n' % newtmp)
-               self.temp_warned = True          
-        outpdf = '%s_compressed' % inpdf
-        cl = ["gs", "-sDEVICE=pdfwrite", "-dNOPAUSE", "-dUseCIEColor", "-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)
-        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:
-             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://getgalaxy.org/" /> 
-        <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').read()
-                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">rgToolFactory.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/rgedgeRpaired_nocamera.xml	Fri Apr 10 22:46:53 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1049 +0,0 @@
-<?xml version="1.0"?>
-<tool id="rgdifferentialcount" name="Differential_Count" version="0.28">
-  <description>models using BioConductor packages</description>
-  <requirements>
-    <requirement type="package" version="3.1.2">R</requirement>
-    <requirement type="package" version="1.3.18">graphicsmagick</requirement>
-    <requirement type="package" version="9.10">ghostscript</requirement>
-    <requirement type="package" version="2.14">biocbasics</requirement>
-  </requirements>
-  <command interpreter="python">
-     rgToolFactory.py --script_path "$runme" --interpreter "Rscript" --tool_name "Differential_Counts" 
-    --output_dir "$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" force_select="True">
-      <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" force_select="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="10" size="3" label="prior.df for tagwise dispersion - larger value = more squeezing of tag dispersions to common dispersion. Replaces prior.n  and prior.df = prior.n * residual.df" help="10 = edgeR default. Use a larger value to 'smooth' small samples. See edgeR docs and note below"/>
-        <param name="edgeR_robust_method" type="select" value="20" size="3" label="Use robust dispersion method" help="Use ordinary, anscombe or deviance robust deviance estimates">
-          <option value="ordinary" selected="true">Use ordinary deviance estimates</option>
-          <option value="deviance">Use robust deviance estimates</option>
-          <option value="anscombe">use Anscombe robust deviance estimates</option>
-        </param>
-      </when>
-      <when value="F"/>
-    </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="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="edgeR_robust" value="ordinary"/>
-      <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" lines_diff="20"/>
-      <output name="html_file" file="edgeRtest1out.html" compare="diff" lines_diff="20"/>
-    </test>
-  </tests>
-  <configfiles>
-    <configfile name="runme"><![CDATA[
-# 
-# edgeR.Rscript
-# updated feb 2014 adding outlier-robust deviance estimate options by ross for R 3.0.2/bioc 2.13
-# 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("gplots")
-library("edgeR")
-library('stringr')
-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(myDGEList,deTags, outSmear, outMain)
-        {
-        pdf(outSmear)
-        plotSmear(myDGEList,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('@@@ Library size 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='log2 raw counts')
-        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('log2 counts 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 = "Differential_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(),TreatmentName="Rx",ControlName="Ctrl",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",robust_meth='ordinary') 
-{
-
-logf = file('Differential.log', open = "a")
-sink(logf,type = c("output", "message"))
-
-
-run_edgeR = function(workCM,pdata,subjects,group,priordf,robust_meth,mydesign,mt,cmrowsums,out_edgeR,nonzerod)
-{
-  logf = file('edgeR.log', open = "a")
-  sink(logf,type = c("output", "message"))
-  #### Setup myDGEList object
-  myDGEList = DGEList(counts=workCM, group = group)
-  myDGEList = calcNormFactors(myDGEList)
-  if (robust_meth == 'ordinary') {
-       myDGEList = estimateGLMCommonDisp(myDGEList,mydesign)
-       myDGEList = estimateGLMTrendedDisp(myDGEList,mydesign)
-       if (priordf > 0) {  myDGEList = estimateGLMTagwiseDisp(myDGEList,mydesign,prior.df = priordf) 
-       } else { myDGEList = estimateGLMTagwiseDisp(myDGEList,mydesign) }
-       comdisp = myDGEList\$common.dispersion
-       estpriorn = getPriorN(myDGEList)
-       print(paste("Common Dispersion =",comdisp,"CV = ",sqrt(comdisp),"getPriorN = ",estpriorn),quote=F)
-     } else { 
-       myDGEList = estimateGLMRobustDisp(myDGEList,design=mydesign, prior.df = priordf, maxit = 6, residual.type = robust_meth)
-          }
-    
-  
-  DGLM = glmFit(myDGEList,design=mydesign)
-  DE = glmLRT(DGLM,coef=ncol(DGLM\$design)) # always last one - subject is first if needed
-  normData = cpm(myDGEList)
-  uoutput = cbind( 
-    Name=as.character(rownames(myDGEList\$counts)),
-    DE\$table,
-    adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
-    Dispersion=myDGEList\$tagwise.dispersion,totreads=cmrowsums,normData,
-    myDGEList\$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(paste("edgeR",mt,"GoodnessofFit.pdf",sep='_'))
-  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()
-  uniqueg = unique(group)
-  write.table(soutput,file=out_edgeR, quote=FALSE, sep="\t",row.names=F)
-  tt = cbind( 
-    Name=as.character(rownames(myDGEList)),
-    DE\$table,
-    adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype),
-    Dispersion=myDGEList\$tagwise.dispersion,totreads=cmrowsums
-  )
-  tt = cbind(tt,URL=contigurls) # add to end so table isn't laid out strangely
-  stt = tt[order(DE\$table\$PValue),]
-  print.noquote("@@ edgeR Top tags\n")
-  print.noquote(stt[1:50,])
-  deTags = rownames(uoutput[uoutput\$adj.p.value < fdrthresh,])
-  nsig = length(deTags)
-  print.noquote(paste('@@',nsig,'tags significant at adj p=',fdrthresh))
-  deColours = ifelse(deTags,'red','black')
-  pdf(paste("edgeR",mt,"BCV_vs_abundance.pdf",sep="_"))
-  plotBCV(myDGEList, cex=0.3, main="Biological CV vs abundance")
-  dev.off()
-  dg = myDGEList[order(DE\$table\$PValue),]
-  outpdfname= paste("edgeR",mt,"top_100_heatmap.pdf",sep="_")
-  ocpm = normData[order(DE\$table\$PValue),]
-  ocpm = ocpm[c(1:100),]
-  hmap2(ocpm,TName=TName,group=group,outpdfname=outpdfname,myTitle=paste(myTitle,'Heatmap'))
-  outSmear = paste("edgeR",mt,"smearplot.pdf",sep="_")
-  outMain = paste("Smear Plot for ",TName,' Vs ',CName,' (FDR@',fdrthresh,' N = ',nsig,')',sep='')
-  smearPlot(myDGEList=myDGEList,deTags=deTags, outSmear=outSmear, outMain = outMain)
-  qqPlot(descr=paste(myTitle,'edgeR adj p QQ plot'),pvector=tt\$adj.p.value,outpdf=paste('edgeR',mt,'qqplot.pdf',sep='_'))
-  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()
-  return(list(myDGEList=myDGEList,edgeRcounts=edgeRcounts))
-} ### run_edgeR
-
-
-run_DESeq2 = function(workCM,pdata,subjects,group,out_DESeq2,mt,DESeq_fitType)
-
- {
-    logf = file("DESeq2.log", open = "a")
-    sink(logf,type = c("output", "message"))
-    # 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))
-        }
-    deSeqDatsizefac = estimateSizeFactors(deSEQds)
-    deSeqDatdisp = estimateDispersions(deSeqDatsizefac,fitType=DESeq_fitType)
-    resDESeq = nbinomWaldTest(deSeqDatdisp)
-    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=paste('DESeq2',mt,'qqplot.pdf',sep="_"))
-    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(paste("DESeq2",mt,"dispersion_estimates.pdf",sep='_'))
-    plotDispEsts(resDESeq)
-    dev.off()
-    ysmall = abs(min(rDESeq\$log2FoldChange))
-    ybig = abs(max(rDESeq\$log2FoldChange))
-    ylimit = min(4,ysmall,ybig)
-    pdf(paste("DESeq2",mt,"MA_plot.pdf",sep="_"))
-    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(paste("DESeq2",mt,"sample_distance_plot.pdf",sep="_"))
-    heatmap.2(sdmat,trace="none",main=paste(myTitle,"DESeq2 sample distances"),
-         col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255))
-    dev.off()
-    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(paste("DESeq2",mt,"PCA_plot.pdf",sep="_"))
-         #### wtf - print? Seems needed to get this to work
-         print(ppca)
-         dev.off()
-        }
-    sink()
-    return(DESeqcounts)
-  }
-
-
-run_Voom = function(workCM,pdata,subjects,group,mydesign,mt,out_Voom)
-  {
-    logf = file('VOOM.log', open = "a")
-    sink(logf,type = c("output", "message")) 
-    if (doedgeR == F) {
-        #### Setup myDGEList object
-        myDGEList = DGEList(counts=workCM, group = group)
-        myDGEList = calcNormFactors(myDGEList)
-        myDGEList = estimateGLMCommonDisp(myDGEList,mydesign)
-        myDGEList = estimateGLMTrendedDisp(myDGEList,mydesign) 
-        myDGEList = estimateGLMTagwiseDisp(myDGEList,mydesign)
-    }
-    pdf(paste("VOOM",mt,"mean_variance_plot.pdf",sep='_'))
-    dat.voomed <- voom(myDGEList, mydesign, plot = TRUE, normalize.method="quantil", lib.size = NULL)
-    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=paste('VOOM',mt,'qqplot.pdf',sep='_'))
-    rownames(rvoom) = rownames(workCM)
-    rvoom = cbind(Contig=rownames(workCM),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% rownames(topresults.voom))
-    voomcounts = rep(0, length(allgenes))
-    voomcounts[voomcountsindex] = 1
-    sink()
-    return(voomcounts)
-    }
-
-
-#### data cleaning and analsis control starts here
-
-
-  # Error handling
-  nugroup = length(unique(group))
-  if (nugroup!=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) # half samples
-  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]+)" # ucsc chr:start-end regexp
-  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(paste("@@ Total low count contigs per sample = ",paste(table(lo),collapse=','))) 
-  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)
-  normData = cpm(workCM)*1e6
-  colnames(normData) = paste( colnames(workCM),'N',sep="_")
-  print(paste('Raw sample read totals',paste(colSums(nonzerod,na.rm=T),collapse=',')))
-
-  if (doedgeR == T) {
-      eres = run_edgeR(workCM,pdata,subjects,group,priordf,robust_meth,mydesign,mt,cmrowsums,out_edgeR,nonzerod)
-      myDGEList = eres\$myDGEList
-      edgeRcounts = eres\$edgeRcounts
-      #### Plot MDS
-      sample_colors =  match(group,levels(group))
-      sampleTypes = levels(factor(group))
-      print.noquote(sampleTypes)
-      pdf(paste("edgeR",mt,"MDSplot.pdf",sep='_'))
-      plotMDS.DGEList(myDGEList,main=paste("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()
-      scale <- myDGEList\$samples\$lib.size*myDGEList\$samples\$norm.factors
-      normCounts <- round(t(t(myDGEList\$counts)/scale)*mean(scale))
-      try({boxPlot(rawrs=nzd,cleanrs=log2(normCounts+1),maint='Effects of TMM size normalisation',myTitle=myTitle,pdfname=paste("edgeR",mt,"raw_norm_counts_box.pdf",sep='_'))},T)
-   }
-  if (doDESeq2 == T) {  DESeqcounts = run_DESeq2(workCM,pdata,subjects,group,out_DESeq2,mt,DESeq_fitType) }
-  if (doVoom == T) { voomcounts = run_Voom(workCM,pdata,subjects,group,mydesign,mt,out_Voom) }
-
-
-  if (doCamera) {
-  doGSEA(y=myDGEList,design=mydesign,histgmt=histgmt,bigmt=bigmt,ntest=20,myTitle=myTitle,
-    outfname=paste("GSEA_Camera",mt,"table.xls",sep="_"),fdrthresh=fdrthresh,fdrtype=fdrtype)
-  }
-  counts.dataframe = c()
-  vennmain = 'no venn'
-  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 = paste("Differential_venn",mt,"significant_genes_overlap.pdf",sep="_") 
-      pdf(vennf)
-      vennDiagram(counts.venn,main=vennmain,col="maroon")
-      dev.off()
-    }
-  } #### doDESeq2 or doVoom
-sink()
-}
-#### Done
-]]>
-builtin_gmt = ""
-history_gmt = ""
-history_gmt_name = ""
-out_edgeR = F
-out_DESeq2 = F
-out_Voom = "$out_VOOM"
-edgeR_robust_meth = "ordinary" 
-doDESeq2 = $DESeq2.doDESeq2
-doVoom = $doVoom
-doCamera = F
-doedgeR = $edgeR.doedgeR
-edgeR_priordf = 10
-
-
-#if $doVoom == "T":
-  out_Voom = "$out_VOOM"
-#end if
-
-#if $DESeq2.doDESeq2 == "T":
-  out_DESeq2 = "$out_DESeq2"
-  doDESeq2 = T
-  DESeq_fitType = "$DESeq2.DESeq_fitType"
-#end if
-
-#if $edgeR.doedgeR == "T":
-  out_edgeR = "$out_edgeR"
-  edgeR_priordf = $edgeR.edgeR_priordf  
-  edgeR_robust_meth = "$edgeR.edgeR_robust_method"
-#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')
-<![CDATA[
-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') 
-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)) )             
-group = factor(group, levels=c(ControlName,TreatmentName))
-colnames(Count_Matrix) = paste(group,colnames(Count_Matrix),sep="_")        
-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,TreatmentName=TreatmentName,ControlName=ControlName,
-                 doDESeq2=doDESeq2,doVoom=doVoom,doCamera=doCamera,doedgeR=doedgeR,org=org,
-                 histgmt=history_gmt,bigmt=builtin_gmt,DESeq_fitType=DESeq_fitType,robust_meth=edgeR_robust_meth)
-sessionInfo()
-
-sink()
-]]>
-</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.
-They must be unique and R names or they will be mangled - please read the fine R docs for the rules on identifiers. 
-
-**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>
-  <citations>
-    <citation type="doi">doi: 10.1093/bioinformatics/btp616</citation>
-  </citations>
-</tool>
--- a/test-data/edgeRtest1out.html	Fri Apr 10 22:46:53 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,613 +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://getgalaxy.org/" /> 
-        <title></title> 
-        <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> 
-        </head> 
-        <body> 
-        <div class="toolFormBody"> 
-        
-<div class="infomessage">Galaxy Tool "Differential_Counts" run at 18/02/2015 14:14:12</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_edgeRtest_MA_plot.pdf"><img src="DESeq2_edgeRtest_MA_plot.png" title="Click to download a PDF of DESeq2_edgeRtest_MA_plot.pdf" hspace="5" width="400" 
-                           alt="Image called DESeq2_edgeRtest_MA_plot.pdf"/></a></td>
-
-<td><a href="DESeq2_edgeRtest_PCA_plot.pdf"><img src="DESeq2_edgeRtest_PCA_plot.png" title="Click to download a PDF of DESeq2_edgeRtest_PCA_plot.pdf" hspace="5" width="400" 
-                           alt="Image called DESeq2_edgeRtest_PCA_plot.pdf"/></a></td>
-
-<td><a href="DESeq2_edgeRtest_dispersion_estimates.pdf"><img src="DESeq2_edgeRtest_dispersion_estimates.png" title="Click to download a PDF of DESeq2_edgeRtest_dispersion_estimates.pdf" hspace="5" width="400" 
-                           alt="Image called DESeq2_edgeRtest_dispersion_estimates.pdf"/></a></td>
-</tr>
-<tr>
-<td><a href="DESeq2_edgeRtest_qqplot.pdf"><img src="DESeq2_edgeRtest_qqplot.png" title="Click to download a PDF of DESeq2_edgeRtest_qqplot.pdf" hspace="5" width="400" 
-                           alt="Image called DESeq2_edgeRtest_qqplot.pdf"/></a></td>
-
-<td><a href="DESeq2_edgeRtest_sample_distance_plot.pdf"><img src="DESeq2_edgeRtest_sample_distance_plot.png" title="Click to download a PDF of DESeq2_edgeRtest_sample_distance_plot.pdf" hspace="5" width="400" 
-                           alt="Image called DESeq2_edgeRtest_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       stat        pvalue          padj  NReads                                                                                               URL
-
-Mir122a             Mir122a  10112.31117      10.433687 0.3440661  30.324653 5.425198e-202 4.568017e-199   90428             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a>
-
-Mir192               Mir192 271352.97636       6.994296 0.2346736  29.804353 3.430828e-195 1.444379e-192 2325567               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
-
-Mir149               Mir149    810.35429      -6.947219 0.2752144 -25.242938 1.353995e-140 3.800212e-138    6164               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a>
-
-Mir23a               Mir23a   1289.18043      -3.104596 0.1650418 -18.810968  6.140634e-79  1.292603e-76   10118               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a>
-
-Mir204               Mir204    347.57397      -7.385478 0.4210055 -17.542475  6.790394e-69  1.143502e-66    2601               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a>
-
-Mir10b               Mir10b  27820.40551      -5.122625 0.3095281 -16.549791  1.606588e-61  2.254579e-59  197340               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a>
-
-Mir194-2           Mir194-2    391.65678       5.272315 0.3261217  16.166709  8.660202e-59  1.041699e-56    3570           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a>
-
-Mir181d             Mir181d    275.22797      -3.578479 0.2232474 -16.029209  7.989327e-58  8.408767e-56    2139             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a>
-
-Mir27a               Mir27a   2788.72629      -3.022597 0.1992370 -15.170866  5.514410e-52  5.159037e-50   21886               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a>
-
-Mir181c             Mir181c   2765.96510      -3.678297 0.2459044 -14.958240  1.376168e-50  1.158734e-48   23605             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a>
-
-Mir195               Mir195    519.86200      -3.158968 0.2124717 -14.867713  5.340712e-50  4.088073e-48    3962               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a>
-
-Mir208b             Mir208b   1649.77924     -12.247146 0.8586111 -14.263905  3.673137e-46  2.577318e-44   14756             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a>
-
-Mir1948             Mir1948    263.89527       7.281854 0.5169425  14.086391  4.604994e-45  2.982619e-43    2404             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a>
-
-Mir490               Mir490    220.99790      -8.314250 0.5954353 -13.963315  2.610066e-44  1.569768e-42    1741               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a>
-
-Mir23b               Mir23b   2028.55377      -2.066561 0.1531073 -13.497466  1.618477e-41  9.085049e-40   16387               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23b'>Mir23b</a>
-
-Mir21                 Mir21  26121.31011       2.974199 0.2230949  13.331544  1.517256e-40  7.984558e-39  229120                 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a>
-
-Mir101b             Mir101b   6846.19683       3.823085 0.2899493  13.185354  1.065529e-39  5.277502e-38   59019             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a>
-
-Mir208a             Mir208a    616.76981     -11.025006 0.8475353 -13.008316  1.097341e-38  5.133115e-37    4638             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a>
-
-Dnm3os               Dnm3os    179.61643      -3.289322 0.2559302 -12.852417  8.336403e-38  3.694343e-36    1401               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Dnm3os'>Dnm3os</a>
-
-Mir215               Mir215    152.78082      -3.012902 0.2351528 -12.812528  1.395132e-37  5.873506e-36    1182               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir215'>Mir215</a>
-
-Mir214               Mir214    134.69038      -3.229468 0.2571076 -12.560766  3.469589e-36  1.391140e-34    1048               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir214'>Mir214</a>
-
-Mir203               Mir203    772.92882       1.991755 0.1694325  11.755450  6.620692e-32  2.533919e-30    6739               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir203'>Mir203</a>
-
-Mir499               Mir499    712.45950     -11.716229 1.0177724 -11.511639  1.152660e-30  4.219739e-29    6527               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a>
-
-Mir27b               Mir27b  76478.05753      -1.906131 0.1672784 -11.394959  4.430372e-30  1.554322e-28  625308               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27b'>Mir27b</a>
-
-Mir322               Mir322    899.53469      -3.147196 0.2773005 -11.349407  7.466726e-30  2.514793e-28    7074               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a>
-
-Rabggtb             Rabggtb   2257.19195       1.991117 0.1756753  11.334078  8.896442e-30  2.881079e-28   19535             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a>
-
-Mir143hg           Mir143hg 180217.77425      -2.173582 0.1966899 -11.050806  2.172555e-28  6.775153e-27 1407364           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143hg'>Mir143hg</a>
-
-Mir143               Mir143 179219.35960      -2.174835 0.1975414 -11.009513  3.438555e-28  1.034023e-26 1399819               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143'>Mir143</a>
-
-Mir378               Mir378    483.21548      -3.012592 0.2747646 -10.964266  5.675913e-28  1.647972e-26    4075               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a>
-
-Mir132               Mir132    106.46062      -2.793901 0.2568175 -10.878935  1.452498e-27  4.076678e-26     857               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir132'>Mir132</a>
-
-Mir155               Mir155     57.66182      -3.815683 0.3605552 -10.582799  3.580985e-26  9.726416e-25     463               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir155'>Mir155</a>
-
-Mir24-2             Mir24-2    424.48288      -2.725743 0.2589560 -10.525891  6.563718e-26  1.674743e-24    3470             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir24-2'>Mir24-2</a>
-
-Mir3074-2         Mir3074-2    424.48288      -2.725743 0.2589560 -10.525891  6.563718e-26  1.674743e-24    3470         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3074-2'>Mir3074-2</a>
-
-Mir125b-2         Mir125b-2    493.08516      -2.938770 0.2803125 -10.483910  1.024200e-25  2.536401e-24    3837         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a>
-
-Mir150               Mir150    553.20599      -2.856250 0.2760016 -10.348671  4.243363e-25  1.020832e-23    4229               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir150'>Mir150</a>
-
-Mir182               Mir182    886.79583       5.089394 0.4937848  10.306907  6.557770e-25  1.533789e-23    7189               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a>
-
-Mir148a             Mir148a 118994.46955       2.695116 0.2621094  10.282410  8.458605e-25  1.924904e-23 1002397             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'>Mir148a</a>
-
-Mir199b             Mir199b     47.84725      -5.417036 0.5304738 -10.211694  1.757697e-24  3.894687e-23     370             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a>
-
-Snord104           Snord104   3851.90119       2.396960 0.2371478  10.107451  5.119918e-24  1.105377e-22   33458           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a>
-
-Mir193               Mir193     45.70861       5.113887 0.5386870   9.493243  2.239557e-21  4.714267e-20     421               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir193'>Mir193</a>
-
-Mir200b             Mir200b     87.13638       6.279428 0.6679043   9.401688  5.369454e-21  1.102703e-19     888             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200b'>Mir200b</a>
-
-5430416N02Rik 5430416N02Rik     62.15966       3.116558 0.3399987   9.166382  4.891610e-20  9.806514e-19     564 <a href='http://www.genecards.org/index.php?path=/Search/keyword/5430416N02Rik'>5430416N02Rik</a>
-
-Mir802               Mir802    166.83414       9.771028 1.0750153   9.089199  9.977106e-20  1.953657e-18    1514               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a>
-
-Mir125b-1         Mir125b-1     79.01988      -3.046196 0.3356809  -9.074680  1.140124e-19  2.181783e-18     609         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-1'>Mir125b-1</a>
-
-2610203C20Rik 2610203C20Rik     79.17666      -3.049266 0.3363186  -9.066600  1.227890e-19  2.297519e-18     610 <a href='http://www.genecards.org/index.php?path=/Search/keyword/2610203C20Rik'>2610203C20Rik</a>
-
-Snord91a           Snord91a    168.95251       2.722976 0.3035329   8.970941  2.939927e-19  5.381346e-18    1437           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord91a'>Snord91a</a>
-
-Mir194-1           Mir194-1     71.10636       3.788463 0.4230333   8.955471  3.382877e-19  6.060389e-18     635           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-1'>Mir194-1</a>
-
-Mir181a-1         Mir181a-1     59.53826      -3.173584 0.3580582  -8.863320  7.766622e-19  1.362395e-17     506         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-1'>Mir181a-1</a>
-
-Mir181a-2         Mir181a-2    347.82506      -2.863247 0.3233431  -8.855136  8.358205e-19  1.436247e-17    2817         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181a-2'>Mir181a-2</a>
-
-Mir184               Mir184     32.23796      -4.996780 0.5668564  -8.814896  1.197967e-18  2.017377e-17     247               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'>Mir184</a>
-
-
-</pre>
-
-<div class="toolFormTitle">Differential 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="Differential_rowsum_bar_charts.pdf"><img src="Differential_rowsum_bar_charts.png" title="Click to download a PDF of Differential_rowsum_bar_charts.pdf" hspace="5" width="400" 
-                           alt="Image called Differential_rowsum_bar_charts.pdf"/></a></td>
-
-<td><a href="Differential_venn_edgeRtest_significant_genes_overlap.pdf"><img src="Differential_venn_edgeRtest_significant_genes_overlap.png" title="Click to download a PDF of Differential_venn_edgeRtest_significant_genes_overlap.pdf" hspace="5" width="400" 
-                           alt="Image called Differential_venn_edgeRtest_significant_genes_overlap.pdf"/></a></td>
-</tr>
-
-</table></div>
-
-<div class="toolFormTitle">Differential log output</div>
-
-<pre>
-
-[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] @@ Total low count contigs per sample =  1,1,1,1,1,1,1,1
-
-[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
-
-[1] "Raw sample read totals 2443751,1644652,1682104,1806045,1440960,1341813,2888924,1428365"
-
-[1] heart liver
-
-
-</pre>
-
-<div class="toolFormTitle">Differential log output</div>
-
-<pre>
-
-Attaching package: ‘gplots’
-
-The following object is masked from ‘package:stats’:
-
-    lowess
-
-Loading required package: limma
-
-Loading required package: methods
-
-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 objects are masked from ‘package:parallel’:
-
-    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
-
-The following object is masked from ‘package:limma’:
-
-    plotMA
-
-The following object is masked from ‘package:stats’:
-
-    xtabs
-
-The following objects are masked from ‘package:base’:
-
-    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, 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
-
-Loading required package: GenomeInfoDb
-
-Loading required package: Rcpp
-
-Loading required package: RcppArmadillo
-
-gene-wise dispersion estimates
-
-mean-dispersion relationship
-
-final dispersion estimates
-
-Warning message:
-
-closing unused connection 4 (edgeR.log) 
-
-Warning message:
-
-In sink() : no sink to remove
-
-
-</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_edgeRtest_mean_variance_plot.pdf"><img src="VOOM_edgeRtest_mean_variance_plot.png" title="Click to download a PDF of VOOM_edgeRtest_mean_variance_plot.pdf" hspace="5" width="400" 
-                           alt="Image called VOOM_edgeRtest_mean_variance_plot.pdf"/></a></td>
-
-<td><a href="VOOM_edgeRtest_qqplot.pdf"><img src="VOOM_edgeRtest_qqplot.png" title="Click to download a PDF of VOOM_edgeRtest_qqplot.pdf" hspace="5" width="400" 
-                           alt="Image called VOOM_edgeRtest_qqplot.pdf"/></a></td>
-</tr>
-
-</table></div>
-
-<div class="toolFormTitle">VOOM log output</div>
-
-<pre>
-
-# VOOM top 50
-
-                     Contig      logFC    AveExpr          t      P.Value    adj.P.Val         B  NReads                                                                                               URL
-
-Mir192               Mir192   6.689950 14.4417888  50.335160 1.802287e-16 2.056409e-13 27.414844 2325567               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
-
-Mir208a             Mir208a -10.458438  3.8918506 -29.183545 2.249812e-13 1.283518e-10 19.141041    4638             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208a'>Mir208a</a>
-
-Mir3073             Mir3073   8.318578  2.6485638  25.821264 1.102217e-12 4.192097e-10 18.063600     904             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir3073'>Mir3073</a>
-
-Mir802               Mir802   8.992449  2.9857711  25.195575 1.514327e-12 4.319618e-10 17.906674    1514               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir802'>Mir802</a>
-
-Mir208b             Mir208b -12.256447  4.4678897 -22.360114 7.074494e-12 1.614400e-09 16.920424   14756             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir208b'>Mir208b</a>
-
-Mir499               Mir499 -11.104485  3.8066799 -21.990054 8.769804e-12 1.667724e-09 16.728874    6527               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir499'>Mir499</a>
-
-Mir10b               Mir10b  -4.775768 12.4173688 -21.487387 1.180685e-11 1.924516e-09 17.249348  197340               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir10b'>Mir10b</a>
-
-Mir148a             Mir148a   2.751538 15.4237642  20.289553 2.464883e-11 3.515539e-09 16.455471 1002397             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir148a'>Mir148a</a>
-
-Mir490               Mir490  -8.497742  3.6613221 -18.336110 8.980482e-11 1.138526e-08 13.923237    1741               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir490'>Mir490</a>
-
-Mir122a             Mir122a  10.197963  8.1512374  17.467826 1.663427e-10 1.897970e-08 14.215445   90428             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir122a'>Mir122a</a>
-
-Mir133b             Mir133b  -6.172367  1.3497975 -17.274094 1.916064e-10 1.987481e-08 13.840201     159             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133b'>Mir133b</a>
-
-Mir149               Mir149  -7.041176  6.0886889 -16.861286 2.602547e-10 2.474589e-08 13.714880    6164               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir149'>Mir149</a>
-
-Mir101b             Mir101b   3.837883 10.6216725  15.443054 7.873164e-10 6.910215e-08 13.054350   59019             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir101b'>Mir101b</a>
-
-Mir143               Mir143  -1.912927 16.0353646 -14.922755 1.209475e-09 9.857220e-08 12.374988 1399819               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143'>Mir143</a>
-
-Mir194-2           Mir194-2   5.534694  6.2627211  14.703097 1.455682e-09 1.107289e-07 12.316769    3570           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir194-2'>Mir194-2</a>
-
-Mir23a               Mir23a  -2.905961  8.6431895 -14.558394 1.646894e-09 1.174441e-07 12.339306   10118               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir23a'>Mir23a</a>
-
-Mir1983             Mir1983  -5.612359  1.1061384 -14.266537 2.119488e-09 1.422551e-07 11.743589     101             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1983'>Mir1983</a>
-
-Mir27a               Mir27a  -2.849084 10.0939084 -14.158498 2.329669e-09 1.476752e-07 11.960195   21886               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27a'>Mir27a</a>
-
-Cyp3a25             Cyp3a25   6.312461  1.6425308  13.845627 3.074630e-09 1.846396e-07 11.502713     226             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Cyp3a25'>Cyp3a25</a>
-
-Mir200a             Mir200a   6.129125  1.8320913  13.226966 5.410979e-09 3.086963e-07 10.979834     264             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir200a'>Mir200a</a>
-
-Mir181d             Mir181d  -3.405544  6.3702152 -13.064584 6.300369e-09 3.423201e-07 11.006301    2139             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181d'>Mir181d</a>
-
-Mir153               Mir153  -5.698257  1.5328802 -12.832092 7.856705e-09 3.829623e-07 10.583835     140               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir153'>Mir153</a>
-
-Mir204               Mir204  -7.718081  4.5031856 -12.808496 8.036265e-09 3.829623e-07 10.353229    2601               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir204'>Mir204</a>
-
-Gm5441               Gm5441  -5.716851  1.5430406 -12.806028 8.055298e-09 3.829623e-07 10.562881     142               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Gm5441'>Gm5441</a>
-
-Rabggtb             Rabggtb   2.327908  9.9369857  12.760291 8.416902e-09 3.841474e-07 10.654006   19535             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Rabggtb'>Rabggtb</a>
-
-Mir504               Mir504  -5.122304  0.8161671 -12.391521 1.205304e-08 5.289430e-07 10.144865      69               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir504'>Mir504</a>
-
-Mir133a-1         Mir133a-1  -4.912497  0.7297882 -12.335045 1.274466e-08 5.385801e-07 10.076395      60         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir133a-1'>Mir133a-1</a>
-
-Mir195               Mir195  -2.954216  7.3530970 -12.081859 1.641098e-08 6.603731e-07 10.055879    3962               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir195'>Mir195</a>
-
-Mir27b               Mir27b  -1.496991 14.9464877 -12.059553 1.678424e-08 6.603731e-07  9.674850  625308               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir27b'>Mir27b</a>
-
-Snord52             Snord52   2.631712  9.7652181  11.922618 1.928407e-08 7.334374e-07  9.811774   18059             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord52'>Snord52</a>
-
-Mir322               Mir322  -3.029558  8.1188344 -11.736839 2.333148e-08 8.587488e-07  9.679815    7074               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir322'>Mir322</a>
-
-Mir181c             Mir181c  -3.676262  9.6244506 -11.575598 2.758358e-08 9.835271e-07  9.453057   23605             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir181c'>Mir181c</a>
-
-Mir1948             Mir1948   7.101780  4.7821564  11.471202 3.077353e-08 1.033009e-06  9.233632    2404             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1948'>Mir1948</a>
-
-0610031O16Rik 0610031O16Rik   4.519875  0.7388871  11.470939 3.078205e-08 1.033009e-06  9.284014      78 <a href='http://www.genecards.org/index.php?path=/Search/keyword/0610031O16Rik'>0610031O16Rik</a>
-
-Mir201               Mir201  -4.964105  0.7490919 -11.289794 3.729283e-08 1.210650e-06  9.114028      63               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir201'>Mir201</a>
-
-Mir21                 Mir21   2.746616 13.2835800  11.267331 3.819755e-08 1.210650e-06  8.925217  229120                 <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir21'>Mir21</a>
-
-Mir184               Mir184  -5.569565  2.3521173 -11.190343 4.148052e-08 1.279170e-06  8.854599     247               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir184'>Mir184</a>
-
-1810019D21Rik 1810019D21Rik   5.164581  1.0784751  11.082009 4.662057e-08 1.399844e-06  8.951908     117 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1810019D21Rik'>1810019D21Rik</a>
-
-Mir203               Mir203   2.216791  8.5426169  10.866758 5.896538e-08 1.725115e-06  8.715639    6739               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir203'>Mir203</a>
-
-1110038B12Rik 1110038B12Rik   2.383720 10.6847245  10.832157 6.125623e-08 1.744094e-06  8.573067   37066 <a href='http://www.genecards.org/index.php?path=/Search/keyword/1110038B12Rik'>1110038B12Rik</a>
-
-Snord104           Snord104   2.571210 10.4798167  10.811468 6.267120e-08 1.744094e-06  8.561110   33458           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Snord104'>Snord104</a>
-
-Mir182               Mir182   5.196800  7.2088299  10.640454 7.579543e-08 2.021320e-06  8.545839    7189               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir182'>Mir182</a>
-
-Mir547               Mir547  -4.542934  0.5799793 -10.635980 7.617593e-08 2.021320e-06  8.435473      42               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir547'>Mir547</a>
-
-Mir143hg           Mir143hg  -2.291921 16.3789153 -10.597275 7.955395e-08 2.062978e-06  7.952584 1407364           <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir143hg'>Mir143hg</a>
-
-Scnn1b               Scnn1b  -4.541403  0.5700621 -10.243065 1.190487e-07 3.018546e-06  8.023327      45               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Scnn1b'>Scnn1b</a>
-
-Mir125b-2         Mir125b-2  -2.896115  7.2737925 -10.091091 1.420082e-07 3.522420e-06  7.876068    3837         <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir125b-2'>Mir125b-2</a>
-
-Mir1a-1             Mir1a-1  -4.402568  0.4498447  -9.950346 1.675164e-07 4.066729e-06  7.692790      42             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir1a-1'>Mir1a-1</a>
-
-Mir378               Mir378  -2.733247  7.2964165  -9.922980 1.730212e-07 4.112858e-06  7.672216    4075               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir378'>Mir378</a>
-
-Mir199b             Mir199b  -5.651345  2.8029895  -9.883978 1.812024e-07 4.219426e-06  7.548022     370             <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir199b'>Mir199b</a>
-
-Mir155               Mir155  -4.158272  3.8002361  -9.845490 1.896814e-07 4.328530e-06  7.604112     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_edgeRtest_BCV_vs_abundance.pdf"><img src="edgeR_edgeRtest_BCV_vs_abundance.png" title="Click to download a PDF of edgeR_edgeRtest_BCV_vs_abundance.pdf" hspace="5" width="400" 
-                           alt="Image called edgeR_edgeRtest_BCV_vs_abundance.pdf"/></a></td>
-
-<td><a href="edgeR_edgeRtest_GoodnessofFit.pdf"><img src="edgeR_edgeRtest_GoodnessofFit.png" title="Click to download a PDF of edgeR_edgeRtest_GoodnessofFit.pdf" hspace="5" width="400" 
-                           alt="Image called edgeR_edgeRtest_GoodnessofFit.pdf"/></a></td>
-
-<td><a href="edgeR_edgeRtest_MDSplot.pdf"><img src="edgeR_edgeRtest_MDSplot.png" title="Click to download a PDF of edgeR_edgeRtest_MDSplot.pdf" hspace="5" width="400" 
-                           alt="Image called edgeR_edgeRtest_MDSplot.pdf"/></a></td>
-</tr>
-<tr>
-<td><a href="edgeR_edgeRtest_qqplot.pdf"><img src="edgeR_edgeRtest_qqplot.png" title="Click to download a PDF of edgeR_edgeRtest_qqplot.pdf" hspace="5" width="400" 
-                           alt="Image called edgeR_edgeRtest_qqplot.pdf"/></a></td>
-
-<td><a href="edgeR_edgeRtest_smearplot.pdf"><img src="edgeR_edgeRtest_smearplot.png" title="Click to download a PDF of edgeR_edgeRtest_smearplot.pdf" hspace="5" width="400" 
-                           alt="Image called edgeR_edgeRtest_smearplot.pdf"/></a></td>
-
-<td><a href="edgeR_edgeRtest_top_100_heatmap.pdf"><img src="edgeR_edgeRtest_top_100_heatmap.png" title="Click to download a PDF of edgeR_edgeRtest_top_100_heatmap.pdf" hspace="5" width="400" 
-                           alt="Image called edgeR_edgeRtest_top_100_heatmap.pdf"/></a></td>
-</tr>
-
-</table></div>
-
-<div class="toolFormTitle">edgeR log output</div>
-
-<pre>
-
-[1] Common Dispersion = 0.228651459675839 CV =  0.478175134940995 getPriorN =  3.33333333333333
-
-[1] "No GLM fit outlier genes found\n"
-
-[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  7.737466e-93  2.942816e-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  2.740528e-92  7.817355e-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  3.313429e-76  7.561245e-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  7.930762e-73  1.508166e-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  6.710365e-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 217.22866  3.638312e-49  5.189142e-47 0.12700995  2325567               <a href='http://www.genecards.org/index.php?path=/Search/keyword/Mir192'>Mir192</a>
-
-Mir802               Mir802  11.440805  6.593380 212.88058  3.231647e-48  4.097010e-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  7.883296e-39  6.919108e-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  9.778601e-38  7.969560e-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 147.24792  6.926822e-34  4.649120e-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  1.703813e-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  2.919521e-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 0.06896653     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  5.031521e-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  5.154209e-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  5.723023e-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  2.997457e-19  9.771711e-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  4.809370e-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  3.620939e-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  1.851472e-17  5.029834e-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  5.651423e-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  2.854936e-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  3.100028e-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  5.764005e-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  8.137283e-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 log output</div>
-
-<pre>
-
-## Toolfactory generated command line = Rscript - None None
-
-Got TCols=1 5 6 7; CCols=2 3 4 8
-
-R version 3.1.0 (2014-04-10)
-
-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=en_AU.UTF-8       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   stats     graphics  grDevices utils     datasets  base     
-
-other attached packages:
-
- [1] RColorBrewer_1.1-2        DESeq2_1.4.5              RcppArmadillo_0.4.600.4.0 Rcpp_0.11.4               GenomicRanges_1.16.4      GenomeInfoDb_1.0.2        IRanges_1.22.10           BiocGenerics_0.10.0       stringr_0.6.2             edgeR_3.6.8               limma_3.20.9              gplots_2.16.0            
-
-loaded via a namespace (and not attached):
-
- [1] annotate_1.42.1      AnnotationDbi_1.26.1 Biobase_2.24.0       bitops_1.0-6         caTools_1.17.1       DBI_0.3.1            gdata_2.13.3         genefilter_1.46.1    geneplotter_1.42.0   grid_3.1.0           gtools_3.4.1         KernSmooth_2.23-13   lattice_0.20-29      locfit_1.5-9.1       RSQLite_1.0.0        stats4_3.1.0         survival_2.37-7      XML_3.98-1.1         xtable_1.7-4         XVector_0.4.0       
-
-
-</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>10.5 KB</td></tr>
-<tr class="odd_row"><td><a href="DESeq2_edgeRtest_MA_plot.pdf">DESeq2_edgeRtest_MA_plot.pdf</a></td><td>14.9 KB</td></tr>
-<tr><td><a href="DESeq2_edgeRtest_PCA_plot.pdf">DESeq2_edgeRtest_PCA_plot.pdf</a></td><td>4.9 KB</td></tr>
-<tr class="odd_row"><td><a href="DESeq2_edgeRtest_dispersion_estimates.pdf">DESeq2_edgeRtest_dispersion_estimates.pdf</a></td><td>188.4 KB</td></tr>
-<tr><td><a href="DESeq2_edgeRtest_qqplot.pdf">DESeq2_edgeRtest_qqplot.pdf</a></td><td>12.8 KB</td></tr>
-<tr class="odd_row"><td><a href="DESeq2_edgeRtest_sample_distance_plot.pdf">DESeq2_edgeRtest_sample_distance_plot.pdf</a></td><td>9.4 KB</td></tr>
-<tr><td><a href="Differential.log">Differential.log</a></td><td>1.4 KB</td></tr>
-<tr class="odd_row"><td><a href="Differential_Counts.Rscript">Differential_Counts.Rscript</a></td><td>28.3 KB</td></tr>
-<tr><td><a href="Differential_Counts_error.log">Differential_Counts_error.log</a></td><td>1.6 KB</td></tr>
-<tr class="odd_row"><td><a href="Differential_Counts_runner.log">Differential_Counts_runner.log</a></td><td>1.4 KB</td></tr>
-<tr><td><a href="Differential_rowsum_bar_charts.pdf">Differential_rowsum_bar_charts.pdf</a></td><td>6.3 KB</td></tr>
-<tr class="odd_row"><td><a href="Differential_venn_edgeRtest_significant_genes_overlap.pdf">Differential_venn_edgeRtest_significant_genes_overlap.pdf</a></td><td>9.7 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_edgeRtest_mean_variance_plot.pdf">VOOM_edgeRtest_mean_variance_plot.pdf</a></td><td>18.3 KB</td></tr>
-<tr><td><a href="VOOM_edgeRtest_qqplot.pdf">VOOM_edgeRtest_qqplot.pdf</a></td><td>17.5 KB</td></tr>
-<tr class="odd_row"><td><a href="edgeR.log">edgeR.log</a></td><td>10.4 KB</td></tr>
-<tr><td><a href="edgeR_edgeRtest_BCV_vs_abundance.pdf">edgeR_edgeRtest_BCV_vs_abundance.pdf</a></td><td>17.4 KB</td></tr>
-<tr class="odd_row"><td><a href="edgeR_edgeRtest_GoodnessofFit.pdf">edgeR_edgeRtest_GoodnessofFit.pdf</a></td><td>13.1 KB</td></tr>
-<tr><td><a href="edgeR_edgeRtest_MDSplot.pdf">edgeR_edgeRtest_MDSplot.pdf</a></td><td>4.9 KB</td></tr>
-<tr class="odd_row"><td><a href="edgeR_edgeRtest_qqplot.pdf">edgeR_edgeRtest_qqplot.pdf</a></td><td>15.2 KB</td></tr>
-<tr><td><a href="edgeR_edgeRtest_smearplot.pdf">edgeR_edgeRtest_smearplot.pdf</a></td><td>16.6 KB</td></tr>
-<tr class="odd_row"><td><a href="edgeR_edgeRtest_top_100_heatmap.pdf">edgeR_edgeRtest_top_100_heatmap.pdf</a></td><td>11.2 KB</td></tr>
-</table></div><br/>
-</div></body></html>
-
--- a/test-data/edgeRtest1out.xls	Fri Apr 10 22:46:53 2015 -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	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	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
-Mir208a	-11.8407506325994	8.46501715136261	594.169461788588	3.10454340520719e-131	3.54228402534141e-128	0.0517121951525415	4638	0	0	0	0.539638866040004	789.596577514809	739.374891373071	627.962821069374	673.126883915814	0	0	0	1	1060	956	1693	928
-Mir149	-7.00898388335122	8.86176664758882	484.303208159111	2.47390942083987e-107	1.41136532458914e-104	0.0495993679492896	6164	9.41025046314352	5.51321148265855	4.26049561369029	8.63422185664007	1042.11850183323	868.533475953932	851.254975991856	934.979044577031	25	9	8	16	1399	1123	2295	1289
-Mir208b	-13.2916347677151	9.90594480087289	417.697578727504	7.73746551125031e-93	2.94281604944553e-90	0.105080963479123	14756	0.376410018525741	0	0	0	1526.30508238476	1273.79753775256	3302.64675652788	1563.13408926571	1	0	0	0	2049	1647	8904	2155
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-C430049B03Rik	-1.8464899758755	10.8687796413297	38.2928388747791	6.08856692564224e-10	8.47201812458268e-09	0.079931503727536	25716	751.314396977378	1013.20575470192	438.8310482101	1051.21651104593	3305.87699151955	2835.30162319423	2672.82934945417	2889.80334646617	1996	1654	824	1948	4438	3666	7206	3984
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-Mir700	-3.09486213889015	3.85060319268209	27.6111661963142	1.48320066810297e-07	1.55259813055549e-06	0.226307066995928	177	1.8820500926287	3.67547432177237	1.06512390342257	5.39638866040004	23.8368778117678	39.4436396025383	11.4984332269053	29.0140898239575	5	6	2	10	32	51	31	40
-Snord33	1.27159425930658	7.86760196119859	26.3468118782013	2.8528943672231e-07	2.9592295209105e-06	0.0542381696207445	3442	244.290102023206	366.322274069979	377.586423763302	324.862597356083	140.786559575754	150.813916127352	114.984332269053	137.816926663798	649	598	709	602	189	195	310	190
-Gas5	1.23567952981899	10.6560730401044	26.0110898815602	3.39461792698953e-07	3.48942257179735e-06	0.0543657258304614	24887	2148.92479576345	2360.87967268512	2450.85010177534	2092.1798836371	949.750600312625	774.178102787076	1251.8455529292	866.070581245132	5709	3854	4602	3877	1275	1001	3375	1194
-Hgd	6.15635943194059	3.3051855066134	25.805478087465	3.77615191469294e-07	3.84695476309343e-06	0.625414653476808	137	20.7025510189157	2.45031621451491	37.8118985715013	3.23783319624003	0	0.773404698088987	0	0	55	4	71	6	0	1	0	0
-Mir30e	-1.85723201668597	13.6073354406477	25.4678355895194	4.49819873385973e-07	4.54198650914509e-06	0.121988368132022	186796	5967.60443370709	6574.19840354351	2870.50891972383	6182.10284935429	17494.7785089744	16148.690096098	28479.0226826382	16115.8761927172	15854	10732	5390	11456	23486	20880	76780	22218
-Mir30b	-1.34107822414686	9.39851902833947	25.3163005241748	4.86579339124038e-07	4.87006163105725e-06	0.0650633323804168	10011	494.602764342823	430.030495647367	238.055192414945	363.176956844923	907.291161710413	860.799428973042	1254.07105613441	843.584661631565	1314	702	447	673	1218	1113	3381	1163
-Mir144	-2.55785018805598	10.1640960703833	24.5353302426251	7.29596937300027e-07	7.23887048225505e-06	0.227712790327382	13709	272.144443394111	286.686997098245	177.343129919858	597.380224706285	2855.21102039082	1869.31915528108	389.463060911307	2740.38078387279	723	468	333	1107	3833	2417	1050	3778
-Mir324	-2.28424718120029	4.17315991586526	23.9323140584544	9.97827464621331e-07	9.81483738907706e-06	0.151576006193348	248	3.76410018525741	3.06289526814364	8.52099122738058	8.09458299060006	31.2859021279453	23.2021409426696	36.3498856850553	23.211271859166	10	5	16	15	42	30	98	32
-Mir328	-1.36751360078994	7.40878077961745	23.8145974236434	1.06074960421632e-06	1.03445752000925e-05	0.0692261869474155	2362	114.428645631825	92.4994370979379	66.5702439639108	104.689940011761	297.21607021548	211.912887276382	203.633543276483	265.478921889211	304	151	125	194	399	274	549	366
-Taf1d	1.59487824982501	6.5338407262267	23.4453937084421	1.28510056283136e-06	1.24262690016151e-05	0.0919378142420328	1421	134.378376613689	106.588755331399	181.603625533549	124.116939189201	39.4798288757405	43.3106630929833	57.8630833353942	39.1690212623426	357	174	341	230	53	56	156	54
-Mirlet7b	-1.08960892589426	9.41902411828326	23.4221409290542	1.30072803125888e-06	1.24716864173646e-05	0.0467359778799628	10012	480.299183638845	481.48713615218	348.828078370892	438.186759224483	1000.40396566263	795.060029635478	1106.44601018898	818.922685281201	1276	786	655	812	1343	1028	2983	1129
-Snord72	1.83779702130742	5.33493032320198	23.2713228191634	1.40682045637618e-06	1.33765178393769e-05	0.112824081220373	603	59.8491929455928	62.4830634701303	65.5051200604882	54.5035254700404	15.6429510639726	18.5617127541357	21.1422804494709	11.605635929583	159	102	123	101	21	24	57	16
-Mir141	2.88915086992602	5.67544057110177	23.2108538029321	1.45175647510816e-06	1.3689703620648e-05	0.279514947318835	835	181.806038947933	73.5094864354474	22.9001639235853	64.2170250587605	16.3878534955904	13.1478798675128	5.56375801301867	11.605635929583	483	120	43	119	22	17	15	16
-Proc	7.2162947395869	2.70683026697518	22.904302696314	1.70270284228067e-06	1.59244585495266e-05	0.79639339332096	83	10.5394805187207	1.22515810725746	26.6280975855643	1.61891659812001	0	0	0	0	28	2	50	3	0	0	0	0
-Mir99b	-2.23913504318406	11.5020751055957	22.0783948324964	2.61739097691589e-06	2.42800252411466e-05	0.199042770426019	35086	956.834267092433	1235.57195116914	602.327567385465	1262.21530766757	7677.7093626841	5160.92955034781	1038.93907963102	5277.66293897787	2542	2017	1131	2339	10307	6673	2801	7276
-Mir34a	-2.07114523247402	3.75691724165632	21.9615656791698	2.78165505832062e-06	2.55957130769663e-05	0.123060595591463	180	4.51692022230889	3.67547432177237	5.32561951711286	5.93602752644005	18.6225607904436	20.8819268484026	22.6259492529426	20.3098628767703	12	6	10	11	25	27	61	28
-Mir181b-1	-5.48921274049575	1.27181133630627	21.9354100409501	2.8198251233018e-06	2.57393637254988e-05	0.242122526338128	19	0	0	0	0	3.72451215808872	3.09361879235595	1.85458600433956	3.62676122799469	0	0	0	0	5	4	5	5
-Gm6307	-4.39870684316397	2.18858336553985	21.7305851128332	3.13749011889e-06	2.8411716076615e-05	0.370895152042377	52	0	0	0	1.07927773208001	4.46941458970647	4.64042818853392	10.7565988251694	6.52817021039044	0	0	0	2	6	6	29	9
-Mir221	-1.07812210165091	8.58912556756594	21.6631660567313	3.24971781636147e-06	2.91962836887278e-05	0.048893795855912	5659	293.976224468604	234.005198486174	197.580484084887	262.264488895442	548.993092102278	473.32367523046	625.366400663298	438.112756341758	781	382	371	486	737	612	1686	604
-Mtmr2	-2.22116729273821	5.29859867913154	21.4813923409378	3.57278772786069e-06	3.18480531053832e-05	0.18432277529643	580	7.52820037051481	9.18868580443092	22.9001639235853	14.5702493830801	49.9084629183889	54.9117335643181	102.373147439544	44.2464869815352	20	15	43	27	67	71	276	61
-Mir30d	-1.57005056457946	13.4267132944328	21.4496922921057	3.63234307687171e-06	3.21279337264389e-05	0.105319951125737	161730	6034.9818270232	6672.21105212411	3115.48741751102	6369.89717473621	15507.3788214182	14583.3189871659	21344.8012411448	14456.9956070324	16033	10892	5850	11804	20818	18856	57546	19931
-Mir17hg	1.27210083938328	13.2259422744804	21.2189405663945	4.09695754137308e-06	3.59586811900514e-05	0.0709557702933317	145451	12165.5717987519	14813.3866748499	13237.3598717357	13978.8051859003	5533.13526205661	5174.07743021532	5994.39288322631	5737.5362626876	32320	24182	24856	25904	7428	6690	16161	7910
-1700003L19Rik	-5.61066488612208	1.40157648597084	21.0598932119004	4.4514850884211e-06	3.87720953121258e-05	0.34919246441141	23	0	0	0	0	3.72451215808872	3.09361879235595	4.45100641041494	1.45070449119788	0	0	0	0	5	4	12	2
-Mir92-1	1.2720872815571	13.225932249746	20.8373934890688	4.99972207274165e-06	4.32172945833199e-05	0.0722548066218893	145450	12165.5717987519	14813.3866748499	13236.827309784	13978.8051859003	5533.13526205661	5174.07743021532	5994.39288322631	5737.5362626876	32320	24182	24855	25904	7428	6690	16161	7910
-Dcaf11	4.49868505204547	3.00449999491973	20.7186492601044	5.31953855219973e-06	4.56360412636082e-05	0.492589105165483	105	11.668710574298	3.67547432177237	30.3560312475433	4.31711092832003	0.744902431617745	0.773404698088987	0	0.725352245598938	31	6	57	8	1	1	0	1
-Rpph1	1.90981175505879	4.84751487377934	20.6554906016174	5.49792967108673e-06	4.64021182687329e-05	0.132837721679408	430	47.0512523157176	29.4037945741789	54.8538810262625	39.9332760869603	7.44902431617745	11.6010704713348	14.8366880347165	10.8802836839841	125	48	103	74	10	15	40	15
-Snord66	1.1226239681981	8.16257105022181	20.6553802765797	5.4982464790993e-06	4.64021182687329e-05	0.0548575342399813	4212	332.746456376755	424.517284164709	429.777495031008	375.588650763843	198.888949241938	217.326720163005	126.11184829509	176.985947926141	884	693	807	696	267	281	340	244
-Mir186	-1.32751183499258	10.3693859127252	20.6440639957771	5.53083968847298e-06	4.64021182687329e-05	0.0788254367296273	18235	766.747207736934	878.438362903596	393.030720362929	976.206708666368	2193.73766111426	1868.54575058299	1537.45179759749	1966.42993781872	2037	1434	738	1809	2945	2416	4145	2711
-Mirlet7i	-1.23644015248455	10.7623495817031	20.542325571297	5.83271631193589e-06	4.85775862183858e-05	0.06908811382823	26242	950.435296777495	923.156633818493	1190.27596207472	1074.42098228565	2244.39102646426	1862.35851299828	3632.76306530032	2008.50036806346	2525	1507	2235	1991	3013	2408	9794	2769
-Mir1960	-3.97365882122643	1.82974168570486	19.776538124304	8.70446255456411e-06	7.19695056141859e-05	0.280749037729358	36	0	0	0.532561951711286	0.539638866040004	4.46941458970647	5.41383288662291	5.56375801301867	4.35211347359363	0	0	1	1	6	7	15	6
-Atf5	6.49323151909569	2.13557412776247	19.5695858043736	9.70011598093827e-06	7.96246930521624e-05	0.721655869824855	50	6.39897031493759	0.612579053628728	14.3791726962047	2.69819433020002	0	0	0	0	17	1	27	5	0	0	0	0
-Fth1	4.14496388894126	5.33212345411694	19.1785400362061	1.19044198050794e-05	9.64262526431375e-05	0.631358500297813	625	74.5291836680967	4.2880533754011	199.710731891732	9.71349958872008	5.95921945294196	3.09361879235595	4.08008920954702	2.90140898239575	198	7	375	18	8	4	11	4
-Mir34b	-4.03579710334289	2.21737061689032	19.1766917106495	1.19159523424035e-05	9.64262526431375e-05	0.403917173086166	54	1.12923005557722	0	0	0	5.95921945294196	4.64042818853392	11.4984332269053	4.35211347359363	3	0	0	0	8	6	31	6
-Sqrdl	5.07655377009118	2.95301443223245	19.0197608961824	1.2937170707173e-05	0.000103952899837214	0.68071739105122	102	13.1743506484009	2.45031621451491	30.8885931992546	1.61891659812001	0.744902431617745	0	0.370917200867911	0	35	4	58	3	1	0	1	0
-Snord45c	1.4432199153589	6.54590578991927	18.6575664995396	1.56425252975082e-05	0.000124812037513684	0.0960670275065403	1427	121.580435983814	129.86675936929	171.484948451034	114.403439600481	42.4594386022115	37.8968302063604	70.4742681649032	44.9718392271341	323	212	322	212	57	49	190	62
-Mirlet7d	-1.15886915037941	10.1553667280072	18.6087995434478	1.60478097214465e-05	0.00012715660341785	0.0670472589616927	16847	796.860009218993	805.541455521777	424.451875513895	793.269133078806	1551.63176505976	1334.1231042035	2002.95288468672	1407.18335646194	2117	1315	797	1470	2083	1725	5400	1940
-Mir137	5.73150408678225	1.59255424435437	18.5911157306787	1.61973651193845e-05	0.000127456507594605	0.435648538321561	29	4.89333024083463	4.90063242902982	1.06512390342257	3.23783319624003	0	0	0	0	13	8	2	6	0	0	0	0
-Cyp2d13	6.2738810929731	1.9910175584115	18.5607585548684	1.64573734247363e-05	0.000128615500531672	0.695708126875112	44	7.15179035198907	0.612579053628728	10.6512390342257	2.15855546416002	0	0	0	0	19	1	20	4	0	0	0	0
-Mir292	6.13636226512856	1.90737366632213	18.3724337687677	1.81667310600165e-05	0.000141008436322985	0.645863676668432	41	9.41025046314352	4.90063242902982	0.532561951711286	3.77747206228003	0	0	0	0	25	8	1	7	0	0	0	0
-Mir320	-1.41780767592226	6.77936159714582	18.1473156510412	2.04457430629556e-05	0.000157625627262381	0.0970223951252841	1651	68.5066233716848	64.9333796846452	42.6049561369029	60.9791918625205	135.57224255443	127.611775184683	238.499760158067	130.563404207809	182	106	80	113	182	165	643	180
-Mir190	-2.0618667114729	3.5998220294058	18.0095366353464	2.19801079041353e-05	0.000168317470594754	0.152993290680449	163	3.76410018525741	5.51321148265855	2.66280975855643	5.39638866040004	14.8980486323549	14.6946892636907	24.1096180564142	18.1338061399734	10	9	5	10	20	19	65	25
-Eci2	6.94390419354011	2.48959191851546	17.7164295795865	2.56402469975373e-05	0.000195036812161267	1.07311229890666	69	9.41025046314352	1.83773716088618	21.8350400201627	0	0	0	0	0	25	3	41	0	0	0	0	0
-Gm10768	6.67795356804963	2.30119145986701	17.5669612528975	2.77365646287063e-05	0.000209585564512277	0.965376367909278	59	9.78666048166926	0	15.4442965996273	2.15855546416002	0	0	0	0	26	0	29	4	0	0	0	0
-0610005C13Rik	4.33430685796504	3.22549471895908	17.5287364390261	2.82997922812616e-05	0.000211677619286898	0.608471609829089	126	15.0564007410296	3.67547432177237	37.27933661979	3.23783319624003	0	1.54680939617797	0	1.45070449119788	40	6	70	6	0	2	0	2
-Snord16a	2.55193916819121	4.59154279853516	17.5230560413965	2.83844660393474e-05	0.000211677619286898	0.284272078731043	368	51.1917625195007	14.7018972870895	69.2330537224672	16.1891659812001	3.72451215808872	3.86702349044493	10.7565988251694	6.52817021039044	136	24	130	30	5	5	29	9
-Tmem205	4.17237062275858	3.00561070371572	17.2103087557158	3.34615664624069e-05	0.00024791978788056	0.565035895318826	106	13.1743506484009	2.45031621451491	30.3560312475433	3.23783319624003	1.48980486323549	0	0.370917200867911	0.725352245598938	35	4	57	6	2	0	1	1
-Snord4a	1.53801116005502	6.21817544635495	17.0751119359038	3.59300925446435e-05	0.000264491842538311	0.118420243290384	1151	121.95684600234	120.065494511231	87.8727220323622	103.071023413641	37.2451215808872	30.1627832254705	57.4921661345263	22.4859196135671	324	196	165	191	50	39	155	31
-Mir3107	-1.51664159875226	10.2873979799643	16.9393351867734	3.85935217489412e-05	0.000282276976381679	0.124378994176375	16873	296.987504616809	380.41159230344	1067.78671318113	843.995186486567	1945.68515138555	2140.78420431032	1468.46119823606	1853.27498750529	789	621	2005	1564	2612	2768	3959	2555
-Mir486	-1.51664148007228	10.2873979799643	16.9213390073356	3.8961128300172e-05	0.000283150620321632	0.12451180656855	16873	296.987504616809	380.41159230344	1067.78671318113	843.995186486567	1945.68515138555	2140.78420431032	1468.46119823606	1853.27498750529	789	621	2005	1564	2612	2768	3959	2555
-Snhg1	0.980597513899204	11.2837096888593	16.9017688457556	3.93648828228718e-05	0.000284274248739853	0.0533948528193988	37837	3080.91600163319	3546.83272051034	3449.93632318571	3151.49097767362	1696.1428367936	1460.9614746901	1889.82313842201	1655.97917670237	8185	5790	6478	5840	2277	1889	5095	2283
-Mir674	-1.82542509566075	4.82285792788346	16.8672226831608	4.00879027316649e-05	0.000287674824005218	0.155466064005568	392	9.41025046314352	13.476739179832	5.85818146882415	19.9666380434802	51.3982677816244	34.0298067159154	48.9610705145643	37.7183167711448	25	22	11	37	69	44	132	52
-2610019E17Rik	1.62113501138988	5.89267132002437	16.8268839562202	4.09490698624491e-05	0.00029201805445659	0.131012768252504	892	93.3496845943837	120.065494511231	52.191071267706	83.6440242362007	33.5206094227985	17.0149033579577	31.8988792746404	30.4647943151554	248	196	98	155	45	22	86	42
-Mir291a	5.48313063221466	1.42869805781767	16.6950147230505	4.38961994130476e-05	0.000311090456709859	0.4318732057878	24	3.76410018525741	4.90063242902982	2.13024780684514	1.07927773208001	0	0	0	0	10	8	4	2	0	0	0	0
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-2310001H17Rik	3.58428400418997	2.24442690645195	16.0087482179931	6.30504687556069e-05	0.000425683934024541	0.352731951590775	54	4.89333024083463	5.51321148265855	7.45586732395801	8.09458299060006	0	0	0	2.17605673679681	13	9	14	15	0	0	0	3
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-4930581F22Rik	4.27156743666311	1.71729906230074	15.4593375711245	8.42994244388826e-05	0.000546509336845256	0.399514955317157	33	3.76410018525741	1.83773716088618	6.92330537224672	3.23783319624003	0	0	0.370917200867911	0	10	3	13	6	0	0	1	0
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-6430411K18Rik	-5.31898602947628	1.18068438167062	15.2786045252782	9.27612572972748e-05	0.000591288237855813	0.575163809877815	17	0	0	0	0	0.744902431617745	1.54680939617797	1.85458600433956	6.52817021039044	0	0	0	0	1	2	5	9
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-Mir340	1.07425135198982	8.56601383462481	12.31506260555	0.000449317639619792	0.00236254113735568	0.0864547028477501	5906	452.821252286466	452.083341578001	734.935493361575	407.427343860203	214.531900305911	184.070318145179	392.43039851825	178.436652417339	1203	738	1380	755	288	238	1058	246
-Gm15787	4.81965375867378	1.03182680206019	12.2510710021598	0.000464991193950011	0.00243373831328882	0.406167431652096	14	0.752820037051481	3.67547432177237	1.06512390342257	2.15855546416002	0	0	0	0	2	6	2	4	0	0	0	0
-Mir878	4.64926579956119	0.974349957697144	12.1747169280425	0.000484416505031649	0.00252383211069001	0.291223458606119	13	1.12923005557722	0.612579053628728	2.66280975855643	2.15855546416002	0	0	0	0	3	1	5	4	0	0	0	0
-Mir668	-3.52129994082869	1.08090432140149	12.1407471573304	0.000493320083968986	0.0025585373445846	0.207929799163555	15	0.376410018525741	0	0	0	2.97960972647098	1.54680939617797	1.85458600433956	2.17605673679681	1	0	0	0	4	2	5	3
-Tardbp	3.26639735890814	2.17673793517601	12.064822750852	0.000513821949169581	0.00265280924888006	0.464336478347876	52	6.77538033346333	4.2880533754011	10.6512390342257	1.61891659812001	0	0.773404698088987	1.11275160260373	0	18	7	20	3	0	1	3	0
-Snhg8	1.68922702390609	3.59241000016082	12.0323448395144	0.000522852600830631	0.00268727395291779	0.153879783916384	164	15.8092207780811	22.0528459306342	10.1186770825144	17.8080825793201	5.21431702132421	3.86702349044493	5.19284081215076	5.8028179647915	42	36	19	33	7	5	14	8
-D830015G02Rik	-4.00371870378144	1.28556444411428	11.8850469968861	0.000565863977044946	0.00289529505743625	0.531321627547781	19	0	0	0	0.539638866040004	2.23470729485323	3.86702349044493	0.741834401735823	5.8028179647915	0	0	0	1	3	5	2	8
-Mir450b	-1.66996632917487	3.92884750600962	11.8198719821002	0.000586018891401928	0.00298503372807857	0.172866406805677	205	6.39897031493759	11.6390020189458	2.13024780684514	7.55494412456006	25.3266826750033	20.8819268484026	24.8514524581501	16.6831016487756	17	19	4	14	34	27	67	23
-Mir98	-0.972268646440252	8.07481173834386	11.790543849501	0.000595323411176222	0.00301895116512031	0.0735460142472877	4140	204.014230040951	156.820237728954	162.431395271942	201.824935898962	303.175289668422	273.785263123501	560.826807712282	282.887375783586	542	256	305	374	407	354	1512	390
-Fam120b	3.7513124511115	1.86837805067541	11.7409122306832	0.000611410483021212	0.00308681133242125	0.569615866291259	39	6.02256029641185	2.45031621451491	7.98842927566929	1.07927773208001	0	0	0.741834401735823	0	16	4	15	2	0	0	2	0
-Bmp1	3.66149432091538	1.8801824905183	11.6658634472443	0.000636573918685723	0.00319969533577273	0.530656556818635	39	4.89333024083463	1.83773716088618	9.58611513080315	1.61891659812001	0	0.773404698088987	0.370917200867911	0	13	3	18	3	0	1	1	0
-Snora24	1.63741748625611	3.55764726367568	11.4974640130802	0.000696912097475758	0.00348761711938526	0.149950706884888	160	15.8092207780811	20.215108769748	10.1186770825144	17.2684437132801	5.21431702132421	3.86702349044493	5.19284081215076	5.8028179647915	42	33	19	32	7	5	14	8
-1700001L05Rik	4.88144873590408	1.10745614758089	11.4650726209799	0.000709164596864133	0.00353343582979029	0.573423120148999	16	2.25846011115444	0	3.19537171026772	2.15855546416002	0	0	0	0	6	0	6	4	0	0	0	0
-2700038G22Rik	-1.25849182157754	5.88412568701528	11.4274331648727	0.000723675925491316	0.0035900618738504	0.119235436031334	872	33.8769016673167	35.5295851104662	36.2142127163675	31.2990542303202	80.4494626147164	77.3404698088987	119.435338679467	49.3239527007278	90	58	68	58	108	100	322	68
-Slc25a44	2.74553045634907	2.63138227225825	11.2881477135035	0.000780034668168989	0.00385289851247107	0.401109003763254	77	8.2810204075663	1.83773716088618	17.5745444064724	5.93602752644005	1.48980486323549	0.773404698088987	1.11275160260373	1.45070449119788	22	3	33	11	2	1	3	2
-Il15ra	3.00551920736697	2.65160751389579	11.2720227223837	0.000786839468546141	0.00386975790349632	0.509183428947547	78	6.77538033346333	8.57610675080219	18.1071063581837	2.15855546416002	1.48980486323549	0	2.22550320520747	0	18	14	34	4	2	0	6	0
-1810026B05Rik	4.75071736662572	1.05600706004695	11.1589283457722	0.000836282173336501	0.00409527021363497	0.515986885031418	15	3.01128014820593	0.612579053628728	2.66280975855643	0.539638866040004	0	0	0	0	8	1	5	1	0	0	0	0
-Mtfr1	3.73003225422438	1.91330931155963	11.1142370903742	0.000856675558071242	0.00417720859726191	0.613480486148045	40	3.76410018525741	1.22515810725746	11.7163629376483	2.15855546416002	0	0.773404698088987	0.370917200867911	0	10	2	22	4	0	1	1	0
-Def8	4.9078971004734	1.11114655162227	11.0965318780522	0.000864893111057709	0.00419933208390147	0.649697634051191	16	1.8820500926287	0.612579053628728	4.79305756540158	0.539638866040004	0	0	0	0	5	1	9	1	0	0	0	0
-0610007N19Rik	-1.91109645132926	3.00746728871961	11.0514352180477	0.00088618570734549	0.00428448259356442	0.213195586418293	104	3.76410018525741	1.22515810725746	3.19537171026772	3.23783319624003	12.6633413375017	8.50745167897886	15.5785224364523	7.25352245598938	10	2	6	6	17	11	42	10
-Mir222	-0.996993817466121	6.95463686071109	10.9709990368329	0.000925488529598804	0.00445562199270985	0.0807689645668732	1840	94.8553246684867	89.4365418297943	64.9725581087769	79.3269133078806	174.307168998552	128.385179882772	218.099314110332	134.190165435803	252	146	122	147	234	166	588	185
-1810008I18Rik	5.51339780558776	1.46232515362208	10.9112063411294	0.000955842599218997	0.00458242187272637	1.17648456256464	25	3.01128014820593	0	8.52099122738058	0.539638866040004	0	0	0	0	8	0	16	1	0	0	0	0
-Hspa13	4.5335645533697	0.923155569802891	10.8598779959922	0.000982701686968161	0.00468178669437989	0.364299931981218	12	1.12923005557722	0.612579053628728	3.19537171026772	1.07927773208001	0	0	0	0	3	1	6	2	0	0	0	0
-Tysnd1	4.67245989477326	0.97728986546695	10.8559741340813	0.000984775465951948	0.00468178669437989	0.482797884010766	13	0.752820037051481	0.612579053628728	3.727933661979	1.61891659812001	0	0	0	0	2	1	7	3	0	0	0	0
-Syce2	5.60456215929371	1.50299640923642	10.8209113982434	0.00100360073571764	0.00475148730063828	1.26696371510068	26	2.25846011115444	0	10.1186770825144	0.539638866040004	0	0	0	0	6	0	19	1	0	0	0	0
-4732471J01Rik	2.22905943203308	2.65196176434118	10.7525538828473	0.00104135515104179	0.00490986044354827	0.261444787613366	78	9.41025046314352	6.12579053628728	7.45586732395801	9.71349958872008	2.97960972647098	0	1.11275160260373	2.90140898239575	25	10	14	18	4	0	3	4
-Mir551b	4.26611873811836	0.813539566342934	10.7376042405193	0.00104980157767058	0.00492931522684007	0.146325189223813	10	1.50564007410296	1.22515810725746	0.532561951711286	1.61891659812001	0	0	0	0	4	2	1	3	0	0	0	0
-Trmt61b	4.96768908260398	1.18270780146598	10.7120149668366	0.00106442045447841	0.00497747433836011	0.773738385816233	18	4.14051020378315	1.22515810725746	2.66280975855643	0	0	0	0	0	11	2	5	0	0	0	0	0
-Mir128-2	-3.78373754460975	1.78339732783065	10.6675010947578	0.00109034319516357	0.00507788402319035	0.714609405508328	35	0	0.612579053628728	0	0.539638866040004	3.72451215808872	0	6.6765096156224	7.25352245598938	0	1	0	1	5	0	18	10
-Mir1b	-3.85021280938259	1.37783937763947	10.6302573175364	0.00111252233588625	0.00516011376116344	0.587543400081271	23	0	0	0	0.539638866040004	1.48980486323549	0.773404698088987	5.93467521388658	2.17605673679681	0	0	0	1	2	1	16	3
-Mir1a-2	-3.85009338813081	1.37783937763947	10.6208756298731	0.00111818085816543	0.00516536177800305	0.588513644741315	23	0	0	0	0.539638866040004	1.48980486323549	0.773404698088987	5.93467521388658	2.17605673679681	0	0	0	1	2	1	16	3
-Snord34	1.90390608992014	3.05424390245224	10.5999960963417	0.00113087898816678	0.00519686665966824	0.214688193526965	110	12.7979406298752	12.8641601262033	7.98842927566929	10.2531384547601	2.97960972647098	2.32021409426696	4.82192361128285	0.725352245598938	34	21	15	19	4	3	13	1
-Mir218-1	-4.02966665256278	0.645094641469066	10.5947207831945	0.00113411025263575	0.00519686665966824	0.0535461111609174	7	0	0	0	0	0.744902431617745	0.773404698088987	1.11275160260373	1.45070449119788	0	0	0	0	1	1	3	2
-U05342	3.31281709881397	2.21106562280467	10.5202105759496	0.00118076029080847	0.00538898996724985	0.596379396994932	54	7.52820037051481	1.83773716088618	12.7814868410709	1.61891659812001	0	0.773404698088987	1.11275160260373	0	20	3	24	3	0	1	3	0
-Mir190b	-2.97565754853409	1.252164062092	10.5071478560106	0.00118913656386351	0.00540559688991339	0.232689411631874	19	0	0.612579053628728	0	0.539638866040004	1.48980486323549	2.32021409426696	2.96733760694329	2.90140898239575	0	1	0	1	2	3	8	4
-Mir483	-4.04934244562865	0.651060211291411	10.4898483450381	0.00120032223527343	0.0054347923430436	0.0832379094929332	7	0	0	0	0	0.744902431617745	1.54680939617797	0.741834401735823	1.45070449119788	0	0	0	0	1	2	2	2
-Gm16023	4.53803195644526	2.35992965031332	10.4655843136008	0.00121619073102306	0.00548487598457433	1.15151574664481	61	5.64615027788611	0	21.8350400201627	1.61891659812001	0	0	0.741834401735823	0	15	0	41	3	0	0	2	0
-Snhg7	2.13792964635233	3.65141323422922	10.4572204627846	0.00122170968929734	0.00548807384050498	0.32408606392021	173	12.7979406298752	9.18868580443092	43.6700800403255	7.01530525852006	2.97960972647098	2.32021409426696	5.56375801301867	5.07746571919256	34	15	82	13	4	3	15	7
-Snord65	-2.14580419998505	4.72864529291437	10.2850878951482	0.0013410963129719	0.00600074860039584	0.371398200429932	320	10.9158905372465	10.4138439116884	10.1186770825144	8.09458299060006	55.1227799397131	69.6064228280088	2.96733760694329	49.3239527007278	29	17	19	15	74	90	8	68
-Schip1	-3.88047326506437	1.2021248273388	10.2667049199552	0.00135452505481037	0.00603716049819779	0.61893576322637	17	0	0	0.532561951711286	0	4.46941458970647	4.64042818853392	0.370917200867911	2.17605673679681	0	0	1	0	6	6	1	3
-Mir3098	1.61240704288362	4.18647370891867	10.2460832181305	0.00136975126774415	0.00608126924706643	0.191902479686364	259	24.8430612226989	12.2515810725746	44.735203943748	18.8873603114001	8.93882917941294	11.6010704713348	7.41834401735823	5.07746571919256	66	20	84	35	12	15	20	7
-Bc1	1.71937890140907	6.08233428298449	10.2256826782949	0.00138498469537857	0.00612506797452305	0.251905498525133	1034	119.32197587266	32.4666898423226	206.101475312268	46.4089424794404	37.990024012505	34.0298067159154	19.2876944451314	31.9154988063533	317	53	387	86	51	44	52	44
-Snord123	-1.86495872183134	2.9794457728339	10.2155083973504	0.00139264598961371	0.00613517017046038	0.221948043618808	102	3.76410018525741	1.22515810725746	3.19537171026772	3.23783319624003	11.9184389058839	8.50745167897886	15.5785224364523	6.52817021039044	10	2	6	6	16	11	42	9
-Tmem41a	4.65538966305359	1.01032960633687	10.1935564653453	0.00140932241124598	0.00618475719704486	0.592503832690539	14	2.63487012968019	0	2.66280975855643	1.07927773208001	0	0	0	0	7	0	5	2	0	0	0	0
-Nagpa	2.97352460471786	1.43647698744846	10.0249505636796	0.00154433821273165	0.00675130230163528	0.269287136797172	24	2.25846011115444	3.06289526814364	3.727933661979	2.15855546416002	0.744902431617745	0	0.370917200867911	0	6	5	7	4	1	0	1	0
-Aes	3.23047856240689	3.06910239429643	9.97879755779423	0.00158353061299317	0.00689621537948554	0.724626715256753	113	15.4328107595554	0.612579053628728	31.4211551509659	1.61891659812001	0.744902431617745	0.773404698088987	1.85458600433956	1.45070449119788	41	1	59	3	1	1	5	2
-1810064F22Rik	4.64882868838756	1.00918245201978	9.93892777924956	0.00161819777729863	0.00702039415930697	0.634235826761203	14	3.01128014820593	1.22515810725746	2.13024780684514	0	0	0	0	0	8	2	4	0	0	0	0	0
-Cacnb2	-4.06302355816955	0.65099714984949	9.92842483925426	0.00162745746116179	0.00703382183024849	0.184783458472924	7	0	0	0	0	2.23470729485323	0.773404698088987	0.741834401735823	0.725352245598938	0	0	0	0	3	1	2	1
-Snora16a	1.50286567656058	4.93292122441817	9.91346035637294	0.00164074336933962	0.00706448371477926	0.188843777270739	464	45.5456122416146	26.953478359664	60.1795005433753	37.7747206228003	8.93882917941294	12.3744751694238	27.8187900650933	9.42957919278619	121	44	113	70	12	16	75	13
-Gm8883	4.91911838145189	1.11319601658003	9.89152693526841	0.00166041533081254	0.00712230786638013	0.886810026012036	16	1.50564007410296	0	5.32561951711286	1.07927773208001	0	0	0	0	4	0	10	2	0	0	0	0
-Zfp862	4.91910478654094	1.11319601658003	9.87749568779978	0.00167312503631305	0.00714994631622919	0.889880816099193	16	1.50564007410296	0	5.32561951711286	1.07927773208001	0	0	0	0	4	0	10	2	0	0	0	0
-Snord99	1.35178914626037	7.9464134418647	9.85562974537361	0.00169312831207699	0.00720843061223822	0.169702504217845	3970	350.437727247465	401.239280126817	355.751383743139	299.499570652202	93.8577063838358	61.8723758471189	314.166869135121	78.3380425246853	931	655	668	555	126	80	847	108
-A530013C23Rik	4.67075454704127	1.01144457530478	9.84836850934807	0.00169982444865375	0.00721003604428971	0.669417175490489	14	3.01128014820593	2.45031621451491	0	1.07927773208001	0	0	0	0	8	4	0	2	0	0	0	0
-Mir1249	-1.46196390939424	4.19931305895641	9.82633429512097	0.00172030857927311	0.00726989662574303	0.166204289309281	240	7.15179035198907	17.7647925552331	4.79305756540158	8.63422185664007	29.051194833092	30.1627832254705	19.2876944451314	26.8380330871607	19	29	9	16	39	39	52	37
-Gm10319	4.53304281290706	0.923052521660086	9.77250957165208	0.001771404990574	0.00745820329979681	0.545741897178802	12	1.12923005557722	0.612579053628728	3.727933661979	0.539638866040004	0	0	0	0	3	1	7	1	0	0	0	0
-Mug-ps1	5.60817971617746	1.61849867045231	9.71925937726679	0.00182346983499073	0.00764918780045744	1.55477121145426	31	9.03384044461778	0	3.727933661979	0	0	0	0	0	24	0	7	0	0	0	0	0
-Gm16551	4.354131830696	0.863214695780697	9.68568139447149	0.00185709505580411	0.00776170497682232	0.396645406828964	11	1.8820500926287	0	1.59768585513386	1.61891659812001	0	0	0	0	5	0	3	3	0	0	0	0
-Pglyrp2	5.56628198650274	1.52062717057535	9.66528674604056	0.00187782449715088	0.00781969982207719	1.52860050877878	27	4.51692022230889	0	7.98842927566929	0	0	0	0	0	12	0	15	0	0	0	0	0
-Mir3071	-1.64821204185537	5.6368744677411	9.59854304216309	0.00194731817483709	0.00805540202644394	0.247041989093597	753	49.6861224453978	22.0528459306342	6.92330537224672	14.5702493830801	59.5921945294196	58.778757054763	111.275160260373	64.5563498583055	132	36	13	27	80	76	300	89
-Mir136	-1.64821282525681	5.6368744677411	9.59738565350616	0.00194854597659818	0.00805540202644394	0.247073475820308	753	49.6861224453978	22.0528459306342	6.92330537224672	14.5702493830801	59.5921945294196	58.778757054763	111.275160260373	64.5563498583055	132	36	13	27	80	76	300	89
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-5730420D15Rik	3.97222804994188	0.701295701561391	7.58721426344322	0.00587837155552645	0.0200215580443453	0.432867265310936	8	0.752820037051481	0	2.13024780684514	1.07927773208001	0	0	0	0	2	0	4	2	0	0	0	0
-Mir351	-0.791220728294839	8.686434600189	7.54485648167784	0.00601816154497295	0.020436673579804	0.0773151721858737	5692	274.402903505265	362.034220694578	167.224452837344	402.030955199803	631.677262011848	531.329027587134	382.415634094817	541.838127462407	729	591	314	745	848	687	1031	747
-Dmr	4.72266894934163	1.05558803758301	7.53885908406383	0.00603822659950114	0.0204439660238303	1.38979384685793	15	3.01128014820593	0	0	3.77747206228003	0	0	0	0	8	0	0	7	0	0	0	0
-Adhfe1	2.85699150346561	1.46062082791113	7.51879164068839	0.00610586249546024	0.0205943194240846	0.446927226811189	25	4.14051020378315	1.22515810725746	3.19537171026772	2.15855546416002	1.48980486323549	0	0	0	11	2	6	4	2	0	0	0
-C330022C24Rik	4.76717929604495	1.06084871369595	7.51499870310104	0.00611873294019691	0.0205943194240846	1.44898233464353	15	2.25846011115444	0	4.79305756540158	0	0	0	0	0	6	0	9	0	0	0	0	0
-E430016F16Rik	-3.92267772171697	0.589304299789426	7.50602828635605	0.0061492822263903	0.020604613895228	0.58028646022718	6	0	0	0	0	1.48980486323549	0	0.370917200867911	2.17605673679681	0	0	0	0	2	0	1	3
-Ncaph2	2.98102373733282	1.88565061259885	7.49949808312218	0.0061716190838939	0.020604613895228	0.659954959399969	39	5.26974025936037	3.06289526814364	8.52099122738058	0.539638866040004	0.744902431617745	0	0	1.45070449119788	14	5	16	1	1	0	0	2
-Mir345	-0.894627342814139	6.16636713262709	7.49822987107232	0.00617596665395968	0.020604613895228	0.0930378402533451	1042	66.2481632605304	46.5560080757833	44.2026419920368	41.0125538190403	93.1128039522181	92.0351590725894	101.26039583694	82.6901559982789	176	76	83	76	125	119	273	114
-Rnu12	1.87451010384159	3.86470859463248	7.43579552508771	0.00639390933463532	0.0212695351335828	0.371941033253866	212	35.0061317228939	3.06289526814364	35.1490888129449	7.01530525852006	5.95921945294196	6.18723758471189	4.08008920954702	5.8028179647915	93	5	66	13	8	8	11	8
-Mir92-2	0.834608763223021	7.78846538426593	7.38642500296428	0.0065717981352971	0.0217977374196918	0.0864815557634083	3238	288.330074190717	320.991424101454	163.496519175365	353.463457256203	204.84816869488	150.813916127352	101.631313037808	175.535243434943	766	524	307	655	275	195	274	242
-4933425B07Rik	3.9241982486516	0.695854728705549	7.38105228770181	0.00659145921804928	0.0217995796167949	0.44178457021332	8	1.50564007410296	0.612579053628728	1.59768585513386	0	0	0	0	0	4	1	3	0	0	0	0	0
-Mir297a-3	-2.47936834158659	1.71218145294539	7.32518775000051	0.00679948610255149	0.0224225827832695	0.460398530180141	32	0	0	0.532561951711286	2.15855546416002	3.72451215808872	2.32021409426696	4.45100641041494	5.07746571919256	0	0	1	4	5	3	12	7
-Lrrc28	3.23201673481653	2.36192282906825	7.30137976409521	0.00689016798552931	0.0226561431455013	0.931712651265681	60	4.51692022230889	1.22515810725746	21.3024780684514	1.07927773208001	0	1.54680939617797	0	1.45070449119788	12	2	40	2	0	2	0	2
-Mir378b	-4.0857848555607	0.698687992326907	7.27231991817715	0.00700252992047912	0.0229594443657088	0.958614553596914	8	0	0	0	0	0	2.32021409426696	1.85458600433956	0	0	0	0	0	0	3	5	0
-Mir664	-0.994464145831067	5.49585681483252	7.25649590052302	0.00706450000488604	0.0230962593282951	0.11543888745938	632	28.2307513894306	32.4666898423226	20.2373541650289	37.7747206228003	58.8472920978018	48.7244959796062	57.8630833353942	71.0845200686959	75	53	38	70	79	63	156	98
-G630025P09Rik	3.16936934987257	1.07132330033658	7.25031573802438	0.00708885466881771	0.0231096662203457	0.458358364233334	15	0.752820037051481	0.612579053628728	2.66280975855643	3.23783319624003	0	0	0.370917200867911	0	2	1	5	6	0	0	1	0
-Tmem161b	4.06849315752567	0.709956285202908	7.22072351001558	0.00720666544788455	0.023426795658223	0.6537375740853	8	0	1.22515810725746	1.06512390342257	2.15855546416002	0	0	0	0	0	2	2	4	0	0	0	0
-Snora36b	-0.98973397816555	5.49748452573385	7.18772095874358	0.00734041539782476	0.0237937896844263	0.115485696310988	633	28.6071614079563	32.4666898423226	20.2373541650289	37.7747206228003	58.8472920978018	48.7244959796062	57.8630833353942	71.0845200686959	76	53	38	70	79	63	156	98
-Gm9920	3.58699262965307	0.575929247951925	7.17616858442569	0.00738783103628811	0.0238482783691762	0.0299525985041335	6	0.752820037051481	0.612579053628728	1.06512390342257	0.539638866040004	0	0	0	0	2	1	2	1	0	0	0	0
-Mir3096	3.58698407384378	0.575929247951925	7.17345169592951	0.00739902764477507	0.0238482783691762	0.0306521588390255	6	0.752820037051481	0.612579053628728	1.06512390342257	0.539638866040004	0	0	0	0	2	1	2	1	0	0	0	0
-C130080G10Rik	-3.58121232355974	0.514014595028031	7.16159261372169	0.00744810371892481	0.02393883476984	0.199889699365146	5	0	0	0	0	0	0.773404698088987	0.741834401735823	1.45070449119788	0	0	0	0	0	1	2	2
-Mir449a	-3.54427958355493	0.508395334408893	7.12012766171262	0.00762232784978802	0.0244299889792363	0.172211097229257	5	0	0	0	0	0	0.773404698088987	1.11275160260373	0.725352245598938	0	0	0	0	0	1	3	1
-2310015A10Rik	3.88092555356897	0.691758047831006	7.08655782076413	0.0077664276979463	0.0248221120542205	0.487031614671006	8	1.8820500926287	0	1.06512390342257	0.539638866040004	0	0	0	0	5	0	2	1	0	0	0	0
-Mir3061	-1.44204597140223	3.21903376859713	7.02924964927639	0.00801889456553959	0.0255207005104828	0.204798976981274	119	4.51692022230889	6.12579053628728	1.59768585513386	5.93602752644005	8.19392674779519	14.6946892636907	12.2402676286411	14.5070449119788	12	10	3	11	11	19	33	20
-2410004N09Rik	4.19079569819786	2.11731138088488	7.02682968914942	0.00802973837271107	0.0255207005104828	1.60622005439893	50	8.2810204075663	0	13.8466107444934	0	0	0	0.741834401735823	0	22	0	26	0	0	0	2	0
-AW112010	3.48093740203176	1.74835513330032	6.99861234370609	0.00815729257425538	0.0258540856311816	1.01336863056868	34	3.38769016673167	0	11.183800985937	1.07927773208001	0.744902431617745	0	0.370917200867911	0	9	0	21	2	1	0	1	0
-A730017L22Rik	3.47278151602734	1.32075691711653	6.9378250633152	0.00843916654528549	0.0266733768093372	0.811991991199655	21	2.63487012968019	1.83773716088618	5.32561951711286	0	0.744902431617745	0	0	0	7	3	10	0	1	0	0	0
-9430083A17Rik	3.75755572586871	0.636221593167552	6.87510421819728	0.00874046603686741	0.0275493694697948	0.370716480330013	7	1.12923005557722	0	1.59768585513386	0.539638866040004	0	0	0	0	3	0	3	1	0	0	0	0
-Mir1968	2.22505699076217	1.70917163211724	6.82625175176362	0.00898275777158784	0.0282350595520158	0.343304792798651	33	4.14051020378315	2.45031621451491	4.26049561369029	2.69819433020002	0	0	1.48366880347165	0.725352245598938	11	4	8	5	0	0	4	1
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-Wdr73	3.72874474943047	0.633055243345956	6.74663559887728	0.00939246309205918	0.0293610969535329	0.381176116932071	7	1.50564007410296	0	1.06512390342257	0.539638866040004	0	0	0	0	4	0	2	1	0	0	0	0
-C030037D09Rik	3.7283557444017	0.633055243345956	6.73331978029021	0.00946283223148127	0.0295002502079785	0.385288183337888	7	1.50564007410296	0	1.06512390342257	0.539638866040004	0	0	0	0	4	0	2	1	0	0	0	0
-Mir1947	-1.29225062781324	3.51713179860465	6.72362225848386	0.00951441970987475	0.0295377133586962	0.17637734020581	146	5.64615027788611	9.18868580443092	3.19537171026772	7.01530525852006	16.3878534955904	21.6553315464916	10.7565988251694	13.0563404207809	15	15	6	13	22	28	29	18
-B230206H07Rik	3.72896488407049	0.633160717686267	6.72133586209116	0.00952662446625785	0.0295377133586962	0.390071784390493	7	1.50564007410296	0	0.532561951711286	1.07927773208001	0	0	0	0	4	0	1	2	0	0	0	0
-Mir329	-2.30769827030506	1.21198057502509	6.6682431812755	0.00981458873210659	0.0303480914453486	0.257827607409142	18	0	1.22515810725746	0	0.539638866040004	1.48980486323549	2.32021409426696	2.59642040607538	2.17605673679681	0	2	0	1	2	3	7	3
-Gm16880	3.73564887167009	0.634016524297442	6.65452030088587	0.0098904593606521	0.0304565326670812	0.420760200355054	7	1.50564007410296	0.612579053628728	1.06512390342257	0	0	0	0	0	4	1	2	0	0	0	0	0
-Gm20605	3.73559585478047	0.634016524297442	6.65225446025383	0.00990304436414297	0.0304565326670812	0.421505452357169	7	1.50564007410296	0.612579053628728	1.06512390342257	0	0	0	0	0	4	1	2	0	0	0	0	0
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-Mir146	-0.710385217413554	9.95438463861553	6.60585785691055	0.0101643823203334	0.0310095193248675	0.0720889056183886	13917	800.624109404251	843.521356846759	415.930884286514	948.685126498327	1416.05952250533	1310.14755856274	947.693448217513	1250.50727141257	2127	1377	781	1758	1901	1694	2555	1724
-Mir92b	-1.20464955764474	4.09905235792638	6.51075099430791	0.0107224214798592	0.0326247544227182	0.174535292554225	237	18.820500926287	7.35094864354474	4.79305756540158	7.55494412456006	23.8368778117678	20.8819268484026	22.2550320520747	23.9366241047649	50	12	9	14	32	27	60	33
-Snord32a	0.713154759186002	7.44314472595647	6.43185559681011	0.0112091413533676	0.0340149741600863	0.0718378375211682	2646	190.087059355499	241.356147129719	201.308417746866	225.569046004722	122.16399878531	89.7149449783225	185.829517634824	123.309881751819	505	394	378	418	164	116	501	170
-Snora7a	2.05831817674996	2.65448513034462	6.39898765932659	0.0114185456444799	0.0345585161282535	0.458148105708972	80	11.2923005557722	1.22515810725746	13.8466107444934	4.85674979436004	0.744902431617745	3.09361879235595	2.59642040607538	0.725352245598938	30	2	26	9	1	4	7	1
-Mir1949	-3.76288567906348	0.525471344199101	6.38181349797709	0.0115295565279671	0.0348021798899749	0.754988501707246	5	0	0	0	0	0.744902431617745	0.773404698088987	0	2.17605673679681	0	0	0	0	1	1	0	3
-Rreb1	2.06949507568778	3.06306696391568	6.37701166765809	0.0115607924861958	0.0348043910996025	0.501561562512581	113	17.3148608521841	1.83773716088618	22.367601971874	2.15855546416002	2.23470729485323	3.09361879235595	3.3382548078112	1.45070449119788	46	3	42	4	3	4	9	2
-B430010I23Rik	3.55351468097294	0.571660508506008	6.3544906141278	0.0117084555342437	0.0351404025748002	0.247102671095999	6	1.12923005557722	0	1.06512390342257	0.539638866040004	0	0	0	0	3	0	2	1	0	0	0	0
-A330009N23Rik	-3.6867092751393	0.572526588246057	6.34887399528495	0.0117455825929726	0.0351404025748002	0.748592452363549	6	0	0	0	0	1.48980486323549	0	1.48366880347165	0	0	0	0	0	2	0	4	0
-Mir1191	2.78203182954512	1.72966994996824	6.34597432028139	0.011764797356331	0.0351404025748002	0.684946592726654	34	6.39897031493759	0	5.32561951711286	2.15855546416002	0	0.773404698088987	0.370917200867911	0.725352245598938	17	0	10	4	0	1	1	1
-Gm10791	4.2152909010073	0.811121956733704	6.31476588511987	0.0119736554136196	0.0356708637779113	1.27425151461492	10	1.50564007410296	0	3.19537171026772	0	0	0	0	0	4	0	6	0	0	0	0	0
-Mir19a	1.07983908902361	3.97679686744879	6.30696565561283	0.0120264496203465	0.0357348411896234	0.131590049177405	223	24.8430612226989	14.7018972870895	18.639668309895	19.4269991774402	11.1735364742662	10.8276657732458	9.64384722256569	5.07746571919256	66	24	35	36	15	14	26	7
-2900009J06Rik	4.10958364300506	0.80184621361431	6.21618451938267	0.012658762709386	0.0375159694841802	1.18480450373992	10	2.63487012968019	0	1.59768585513386	0	0	0	0	0	7	0	3	0	0	0	0	0
-Rnu11	1.78240522507142	4.31503812639707	6.21011956935085	0.0127022049994492	0.0375471914621023	0.428450018320618	297	39.146641926677	6.73836958991601	61.7771863985092	4.31711092832003	5.95921945294196	9.28085637706784	11.1275160260373	5.8028179647915	104	11	116	8	8	12	30	8
-Mir29a	-0.77500990655082	11.1527649022789	6.20113244815113	0.0127668602517145	0.0376407946956234	0.0917237176546651	33081	1846.29114086876	2137.90089716426	774.877639739921	1956.73052826106	2932.68087327906	2669.79301780318	3109.76981207657	2779.54980513513	4905	3490	1455	3626	3937	3452	8384	3832
-4931440P22Rik	2.69422554144544	0.922636384440636	6.17634512081849	0.0129469442129526	0.0380549526008401	0.214786057182653	12	1.50564007410296	0.612579053628728	1.06512390342257	2.15855546416002	0.744902431617745	0	0	0	4	1	2	4	1	0	0	0
-4930405P13Rik	4.2497789323049	0.814222276413148	6.17264663574254	0.0129740373021269	0.0380549526008401	1.39750324685157	10	1.12923005557722	0	3.727933661979	0	0	0	0	0	3	0	7	0	0	0	0	0
-Mir666	-2.8061534653004	0.780065908832119	6.10876767067663	0.0134512885456024	0.0393536416167497	0.307684101038399	9	0	0	0	0.539638866040004	1.48980486323549	1.54680939617797	0.370917200867911	2.17605673679681	0	0	0	1	2	2	1	3
-Gm12718	3.58286595198089	0.575822842137927	6.08629627639691	0.0136234373520169	0.0397553504313331	0.387364388499996	6	0.752820037051481	0.612579053628728	1.59768585513386	0	0	0	0	0	2	1	3	0	0	0	0	0
-2700089E24Rik	3.04034763305133	2.50936021306659	6.06545976007677	0.0137850864462438	0.0401244480488883	1.06340957989852	70	10.163070500195	0	19.1722302616063	1.07927773208001	0.744902431617745	0.773404698088987	0	2.17605673679681	27	0	36	2	1	1	0	3
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-Rchy1	2.54271958534832	0.869700915716328	5.03471775694501	0.0248441347275372	0.0618933574762444	0.290422200398644	11	1.50564007410296	0.612579053628728	2.13024780684514	0.539638866040004	0	0.773404698088987	0	0	4	1	4	1	0	1	0	0
-Elp3	-2.02523152584439	2.32944726038921	5.02735599193548	0.024949959626223	0.0618982426664293	0.604793592405098	55	3.76410018525741	0.612579053628728	1.59768585513386	0.539638866040004	12.6633413375017	5.41383288662291	0.741834401735823	10.1549314383851	10	1	3	1	17	7	2	14
-1700003F17Rik	-2.23540184425715	1.12945697891322	5.02703434830282	0.0249545938883063	0.0618982426664293	0.423931938221968	16	0.376410018525741	0	1.06512390342257	0	1.48980486323549	0.773404698088987	1.48366880347165	4.35211347359363	1	0	2	0	2	1	4	6
-4833422C13Rik	2.45936493705799	1.75834534088732	4.98445084831784	0.0255761014710267	0.0633022381311095	0.747806173855609	34	3.38769016673167	3.67547432177237	7.98842927566929	0	1.48980486323549	0.773404698088987	0.370917200867911	0	9	6	15	0	2	1	1	0
-Mir3089	-3.26019061576153	0.441369062904739	4.97890405182039	0.0256582324868572	0.0633680590205716	0.663200412611287	4	0	0	0	0	0	1.54680939617797	0.741834401735823	0	0	0	0	0	0	2	2	0
-BC024582	2.42294846583629	0.815684400444074	4.97391621162486	0.0257323210129772	0.0634137759736653	0.161867609999955	10	1.50564007410296	1.22515810725746	1.06512390342257	0.539638866040004	0.744902431617745	0	0	0	4	2	2	1	1	0	0	0
-Six3os1	-4.46352708702951	0.725197717198738	4.96527105061809	0.0258612616117471	0.0635941799547489	3.10022171650773	8	0	0	0	0	0	0	0	5.8028179647915	0	0	0	0	0	0	0	8
-Mir1938	-3.24656968690343	0.44073775939572	4.94933188451975	0.026100753282661	0.0636493602847117	0.663220377283913	4	0	0	0	0	0.744902431617745	0	0.741834401735823	0.725352245598938	0	0	0	0	1	0	2	1
-Mir384	-3.24656968690343	0.44073775939572	4.94933188451975	0.026100753282661	0.0636493602847117	0.663220377283913	4	0	0	0	0	0.744902431617745	0	0.741834401735823	0.725352245598938	0	0	0	0	1	0	2	1
-Sec14l1	-3.24656968690343	0.44073775939572	4.94933188451975	0.026100753282661	0.0636493602847117	0.663220377283913	4	0	0	0	0	0.744902431617745	0	0.741834401735823	0.725352245598938	0	0	0	0	1	0	2	1
-1700018L02Rik	2.52725439485413	1.2810872988006	4.94237675359851	0.0262059776758415	0.0636493602847117	0.610769737669636	20	3.01128014820593	2.45031621451491	3.19537171026772	0	0.744902431617745	0	0	0.725352245598938	8	4	6	0	1	0	0	1
-4932412D23Rik	-3.24299283757227	0.44056942053285	4.94155729246304	0.0262184043241144	0.0636493602847117	0.663225700951647	4	0	0	0	0	0	0	0.741834401735823	1.45070449119788	0	0	0	0	0	0	2	2
-Smpx	-3.24299283757227	0.44056942053285	4.94155729246304	0.0262184043241144	0.0636493602847117	0.663225700951647	4	0	0	0	0	0	0	0.741834401735823	1.45070449119788	0	0	0	0	0	0	2	2
-Angel2	3.00095434308483	1.56565914609037	4.93642929744956	0.0262963065481261	0.0637029421898342	1.11574431165571	28	3.76410018525741	1.22515810725746	7.45586732395801	0	0	0	0	1.45070449119788	10	2	14	0	0	0	0	2
-Gm16998	2.16934043071096	1.59943008518047	4.89762958680514	0.0268935868563399	0.0650118275489064	0.507140420467609	28	0.752820037051481	4.90063242902982	2.66280975855643	4.85674979436004	0.744902431617745	1.54680939617797	0	0.725352245598938	2	8	5	9	1	2	0	1
-Gm9961	2.48079807981747	0.81113688705366	4.87714628996048	0.0272145769468498	0.0656486940726336	0.238468050975502	10	1.50564007410296	1.83773716088618	0.532561951711286	0.539638866040004	0	0	0.370917200867911	0	4	3	1	1	0	0	1	0
-Gorasp2	2.50323271127873	1.43485825537994	4.86866310220583	0.0273486797562777	0.065821775214044	0.726065774237414	24	1.50564007410296	0.612579053628728	7.45586732395801	1.07927773208001	0	0	0.741834401735823	0.725352245598938	4	1	14	2	0	0	2	1
-Mir1199	-2.1410891017329	0.875152487625875	4.86532083563142	0.0274017030908597	0.065821775214044	0.187465626508598	11	0.376410018525741	0.612579053628728	0	0	2.23470729485323	0.773404698088987	1.48366880347165	0.725352245598938	1	1	0	0	3	1	4	1
-D130020L05Rik	1.99560087261182	2.2275947807044	4.82997707328338	0.027969002552473	0.0670433443537219	0.541921055077734	52	3.01128014820593	7.35094864354474	8.52099122738058	4.31711092832003	2.97960972647098	3.09361879235595	0	0	8	12	16	8	4	4	0	0
-Mir337	-1.62336036905269	2.17305843018542	4.81765541370171	0.0281696374923431	0.0673827177751854	0.346358081824338	50	2.63487012968019	3.06289526814364	0	1.07927773208001	7.44902431617745	5.41383288662291	5.19284081215076	3.62676122799469	7	5	0	2	10	7	14	5
-4930592A05Rik	3.5587501426435	0.574747799479499	4.79177897275975	0.0285958775829413	0.0682591973266444	1.10473049154479	6	0.752820037051481	0	2.13024780684514	0	0	0	0	0	2	0	4	0	0	0	0	0
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-Gm20300	3.55867540528589	0.574747799479499	4.78291720706027	0.0287433884266286	0.068325429572465	1.11166042987322	6	0.752820037051481	0	2.13024780684514	0	0	0	0	0	2	0	4	0	0	0	0	0
-Mir1195	1.18551091024559	3.42829913358875	4.76777468878607	0.0289972834355851	0.0687229212681769	0.210496045969635	144	13.9271706854524	10.4138439116884	21.8350400201627	6.47566639248005	6.7041218845597	4.64042818853392	4.08008920954702	7.97887470158832	37	17	41	12	9	6	11	11
-Gnas	1.62261058729608	3.79700597703784	4.76577018963775	0.0290310675295892	0.0687229212681769	0.451188823352324	198	30.489211500585	1.83773716088618	34.6165268612336	7.01530525852006	5.21431702132421	10.0542610751568	2.59642040607538	6.52817021039044	81	3	65	13	7	13	7	9
-Snord12	0.762314805507956	7.35216142127777	4.74102925020227	0.0294514462766702	0.0695737064216991	0.113004646636548	2566	201.002949892746	232.780040378917	188.526930905795	192.111436310242	85.6637796360407	80.4340886012546	223.292154922483	87.7676217174715	534	380	354	356	115	104	602	121
-C530005A16Rik	2.13294951392173	1.06984389113655	4.73284391790719	0.0295919168507174	0.0696726055972731	0.252138005819299	15	1.8820500926287	0.612579053628728	2.13024780684514	1.61891659812001	0	0.773404698088987	0	0.725352245598938	5	1	4	3	0	1	0	1
-Cd40	-3.1514868709687	0.435092695795631	4.73147733199976	0.0296154370856069	0.0696726055972731	0.66339891116179	4	0	0	0	0	0.744902431617745	0	1.11275160260373	0	0	0	0	0	1	0	3	0
-Mir1970	3.8210089530472	0.642462262502323	4.72103439935654	0.0297958141335944	0.0698632586238908	1.68660268150801	7	0.376410018525741	0	3.19537171026772	0	0	0	0	0	1	0	6	0	0	0	0	0
-Snora52	1.1558427881911	3.02172876320995	4.71970047406193	0.0298189368534924	0.0698632586238908	0.179149701644827	105	9.03384044461778	9.80126485805965	12.2489248893596	7.01530525852006	2.97960972647098	3.09361879235595	4.82192361128285	5.8028179647915	24	16	23	13	4	4	13	8
-Dnajc5	2.44542986944954	1.42647556996213	4.69405295179299	0.0302671745951663	0.0707681274858294	0.714886625520753	24	2.63487012968019	0.612579053628728	6.39074342053543	0.539638866040004	0.744902431617745	0	0.741834401735823	0	7	1	12	1	1	0	2	0
-Mir338	-1.00910007112503	5.11127216101117	4.66844673613115	0.0307217005692248	0.0715778078985726	0.188465090351706	469	22.9610111300702	31.8541107886939	6.92330537224672	28.6008599001202	46.1839507603002	41.7638536968053	33.382548078112	60.9295886303108	61	52	13	53	62	54	90	84
-Mir3065	-1.00910039649793	5.11127216101117	4.667483552064	0.0307389359073625	0.0715778078985726	0.18850778945958	469	22.9610111300702	31.8541107886939	6.92330537224672	28.6008599001202	46.1839507603002	41.7638536968053	33.382548078112	60.9295886303108	61	52	13	53	62	54	90	84
-Mir466g	2.74152413221756	1.83084002981743	4.65940319997969	0.0308839244207391	0.0717689567496197	1.04920834310069	38	9.03384044461778	1.22515810725746	4.79305756540158	0	1.48980486323549	0.773404698088987	0	0	24	2	9	0	2	1	0	0
-Mir495	-2.34021892384841	0.645644470451624	4.61800475521103	0.0316380196083925	0.0733719113275931	0.0931265969200643	7	0.376410018525741	0	0	0	0.744902431617745	1.54680939617797	0.741834401735823	0.725352245598938	1	0	0	0	1	2	2	1
-Mir540	-1.87048592611444	1.47646177493351	4.55637621097871	0.0327963966821609	0.0759040337004982	0.396099074114148	25	1.50564007410296	1.22515810725746	0	0	1.48980486323549	3.09361879235595	2.96733760694329	3.62676122799469	4	2	0	0	2	4	8	5
-2010308F09Rik	-2.32788360610317	0.648937351473606	4.53820265327646	0.0331463778977969	0.0764423431505572	0.102970605180222	7	0	0	0	0.539638866040004	0.744902431617745	1.54680939617797	0.741834401735823	0.725352245598938	0	0	0	1	1	2	2	1
-2900060B14Rik	-1.08100697451938	3.76125731921139	4.53734555183174	0.0331629797191287	0.0764423431505572	0.19805942597192	185	10.163070500195	12.8641601262033	3.19537171026772	5.93602752644005	13.4082437691194	10.8276657732458	21.1422804494709	22.4859196135671	27	21	6	11	18	14	57	31
-1700102H20Rik	-3.0536018712959	0.429297019684393	4.51820972546753	0.0335359059665572	0.0768362825458671	0.663582233184681	4	0	0	0	0	0	0	1.48366880347165	0	0	0	0	0	0	0	4	0
-9230112J17Rik	-3.0536018712959	0.429297019684393	4.51820972546753	0.0335359059665572	0.0768362825458671	0.663582233184681	4	0	0	0	0	0	0	1.48366880347165	0	0	0	0	0	0	0	4	0
-Mir3100	-3.0536018712959	0.429297019684393	4.51820972546753	0.0335359059665572	0.0768362825458671	0.663582233184681	4	0	0	0	0	0	0	1.48366880347165	0	0	0	0	0	0	0	4	0
-D330041H03Rik	3.32930386867045	1.27786048002356	4.50364881692077	0.0338226082894355	0.0773378678521961	1.47504094998204	20	2.63487012968019	0	6.39074342053543	0	0.744902431617745	0	0	0	7	0	12	0	1	0	0	0
-Gm16907	3.26552611692943	0.503997485712753	4.49052448499452	0.0340832193996225	0.0777779066699384	0.74123061571865	5	1.12923005557722	0	1.06512390342257	0	0	0	0	0	3	0	2	0	0	0	0	0
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-Mir466n	2.20067011169102	2.42089442891858	4.45788316389828	0.0347405238793725	0.0789620273831953	0.785648303301501	64	8.65743042609204	2.45031621451491	14.911734647916	0.539638866040004	2.23470729485323	0.773404698088987	0	2.90140898239575	23	4	28	1	3	1	0	4
-Mir139	-0.721194493867096	5.68703734270453	4.45193702955004	0.0348616824471985	0.0790798800641223	0.100083940011654	751	38.7702319081513	40.430217539496	39.4095844266352	33.9972485605203	58.8472920978018	53.3649241681401	80.4890325883368	58.028179647915	103	66	74	63	79	69	217	80
-4930556M19Rik	2.66295078370762	1.38828943045466	4.44749353289719	0.0349525116616738	0.0791286027896226	0.905594146358324	23	4.14051020378315	1.83773716088618	3.727933661979	0	1.48980486323549	0	0	0	11	3	7	0	2	0	0	0
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-Gm19710	3.30854550904047	0.507213862469314	4.43368853866039	0.0352362808229496	0.0794233323118973	0.866290226187716	5	0.752820037051481	0	1.59768585513386	0	0	0	0	0	2	0	3	0	0	0	0	0
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-Gm3219	3.60737493223815	0.577946067919671	4.42147872722661	0.0354892683723821	0.0795040795541247	1.52667717941247	6	0.376410018525741	0	2.66280975855643	0	0	0	0	0	1	0	5	0	0	0	0	0
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-Stap2	1.96836921762168	1.45702826044348	4.24688512420852	0.0393223911574594	0.0865226043831307	0.447793446770992	25	3.76410018525741	0.612579053628728	3.19537171026772	2.15855546416002	0	1.54680939617797	0.741834401735823	0	10	1	6	4	0	2	2	0
-Runx2	-1.8781114233878	1.22110313001472	4.24585642620524	0.0393462199105113	0.0865226043831307	0.341255251954418	18	0	1.83773716088618	0	0.539638866040004	2.23470729485323	1.54680939617797	1.85458600433956	2.90140898239575	0	3	0	1	3	2	5	4
-Mir188	-1.5992225727793	1.98299554425222	4.24251861816951	0.0394236412376492	0.0865226043831307	0.37162947682695	41	1.8820500926287	3.06289526814364	0	1.07927773208001	4.46941458970647	6.18723758471189	2.59642040607538	5.8028179647915	5	5	0	2	6	8	7	8
-Snora61	0.969697226409068	3.56540254224777	4.24140175926445	0.0394495827410303	0.0865226043831307	0.154073484158	164	18.820500926287	12.8641601262033	12.7814868410709	10.7927773208001	7.44902431617745	3.86702349044493	8.53109561996196	7.97887470158832	50	21	24	20	10	5	23	11
-Vsig8	0.750069910158889	5.57576368322374	4.23890276443729	0.0395076922731035	0.0865226043831307	0.113360000973271	711	73.0235435939937	60.6453263092441	39.4095844266352	58.8206363983605	37.2451215808872	27.0691644331145	37.0917200867911	36.2676122799469	194	99	74	109	50	35	100	50
-Ano4	-2.44102696576185	0.940052484741396	4.21583777335836	0.0400482852153068	0.0875384931621937	0.691619616682222	12	0.376410018525741	0	0.532561951711286	0	4.46941458970647	0	0.741834401735823	1.45070449119788	1	0	1	0	6	0	2	2
-Snord37	0.761098097700821	5.37374937014978	4.21175927132711	0.0401446812714905	0.0875814174584525	0.115843179086507	605	50.4389424824493	69.2214330600463	39.4095844266352	43.1711092832003	29.051194833092	24.7489503388476	33.0116308772441	31.9154988063533	134	113	74	80	39	32	89	44
-5430405H02Rik	2.58778573027926	1.29115223901932	4.19097140138208	0.0406398043383035	0.0884923983778708	0.897399733720278	20	2.25846011115444	4.90063242902982	0	2.15855546416002	0	0	0	1.45070449119788	6	8	0	4	0	0	0	2
-Polg2	3.14592319385236	0.445065788409347	4.15497592271059	0.0415123640578155	0.0900486832508887	0.663083507648574	4	0	1.22515810725746	1.06512390342257	0	0	0	0	0	0	2	2	0	0	0	0	0
-Sgsm1	3.14592319385236	0.445065788409347	4.15497592271059	0.0415123640578155	0.0900486832508887	0.663083507648574	4	0	1.22515810725746	1.06512390342257	0	0	0	0	0	0	2	2	0	0	0	0	0
-4930502E09Rik	3.13239036710485	0.444300161259273	4.12791161602774	0.0421813754185719	0.0913262796064337	0.663107719639555	4	0	0.612579053628728	0	1.61891659812001	0	0	0	0	0	1	0	3	0	0	0	0
-Zfp414	3.35771159436211	0.510435203260448	4.12231482263212	0.0423211327778117	0.0913615916084482	1.26204273440625	5	0.376410018525741	0	2.13024780684514	0	0	0	0	0	1	0	4	0	0	0	0	0
-9230116N13Rik	3.12878070152111	0.444084400555259	4.12059660713342	0.042364135867917	0.0913615916084482	0.663114542800526	4	0	0.612579053628728	1.06512390342257	0.539638866040004	0	0	0	0	0	1	2	1	0	0	0	0
-4833417C18Rik	2.35006375536508	0.758568204956497	4.11765359227924	0.0424378996954229	0.0913615916084482	0.280418772686869	9	0.752820037051481	0.612579053628728	0.532561951711286	2.15855546416002	0	0	0.370917200867911	0	2	1	1	4	0	0	1	0
-Gm9999	3.42407156884896	0.514090525834695	4.1097642848848	0.0426363044548118	0.0916158632447086	1.41465663862133	5	0	0	0.532561951711286	2.15855546416002	0	0	0	0	0	0	1	4	0	0	0	0
-Mir191	-0.724056835181733	13.66326713492	4.10168204575712	0.0428405727501232	0.0917658837596602	0.121505261168157	174890	8555.79972109009	11471.1553582516	6973.89875765929	12136.4780972397	19775.6697545879	18076.0146037358	8338.58959271151	18458.7639460018	22730	18726	13095	22490	26548	23372	22481	25448
-Snord88c	0.772003291831522	4.59608010488051	4.09905735191624	0.0429071296822148	0.0917658837596602	0.111637028195874	341	27.8543413709048	25.1157411987778	34.6165268612336	28.0612210340802	21.6021705169146	17.0149033579577	12.9821020303769	16.6831016487756	74	41	65	52	29	22	35	23
-Scarna13	2.37818263258558	0.813784050534841	4.09747140793165	0.0429473987096043	0.0917658837596602	0.357362691777665	10	1.50564007410296	0	1.06512390342257	1.61891659812001	0.744902431617745	0	0	0	4	0	2	3	1	0	0	0
-Mir880	3.11348514900425	0.443211372076721	4.09020920557683	0.0431323031043017	0.0918100652692691	0.663142151271803	4	0	0	0.532561951711286	1.61891659812001	0	0	0	0	0	0	1	3	0	0	0	0
-9330151L19Rik	3.10988480327257	0.442995740899849	4.08298010878458	0.0433171963149346	0.0918100652692691	0.663148970364509	4	0	0	1.59768585513386	0.539638866040004	0	0	0	0	0	0	3	1	0	0	0	0
-Lins	3.10988480327257	0.442995740899849	4.08298010878458	0.0433171963149346	0.0918100652692691	0.663148970364509	4	0	0	1.59768585513386	0.539638866040004	0	0	0	0	0	0	3	1	0	0	0	0
-1190002F15Rik	3.10808521622629	0.442887934784986	4.07937160767517	0.0434098000013034	0.0918100652692691	0.663152379614698	4	0	0	2.13024780684514	0	0	0	0	0	0	0	4	0	0	0	0	0
-Tsix	3.10808521622629	0.442887934784986	4.07937160767517	0.0434098000013034	0.0918100652692691	0.663152379614698	4	0	0	2.13024780684514	0	0	0	0	0	0	0	4	0	0	0	0	0
-Snhg10	2.37733284339775	0.813784050534841	4.07777407135823	0.0434508634929056	0.0918100652692691	0.363056531257187	10	1.50564007410296	0	1.06512390342257	1.61891659812001	0.744902431617745	0	0	0	4	0	2	3	1	0	0	0
-Mir19b-2	1.95460141884699	0.967543811537092	4.06675104167637	0.0437353184442186	0.092240292689193	0.19469836422249	13	1.8820500926287	0.612579053628728	1.06512390342257	1.61891659812001	0	0.773404698088987	0.370917200867911	0	5	1	2	3	0	1	1	0
-4930451G09Rik	3.09940234131107	0.441920006309181	4.05746985698464	0.0439763435004616	0.0924070127698466	0.663182989422171	4	0.376410018525741	1.22515810725746	0	0.539638866040004	0	0	0	0	1	2	0	1	0	0	0	0
-4933421O10Rik	3.09940234131107	0.441920006309181	4.05746985698464	0.0439763435004616	0.0924070127698466	0.663182989422171	4	0.376410018525741	1.22515810725746	0	0.539638866040004	0	0	0	0	1	2	0	1	0	0	0	0
-Icmt	3.04158259524874	1.01298978592042	4.05190601988617	0.0441215017392087	0.0925416056699212	1.3064646184197	14	1.8820500926287	0	4.26049561369029	0	0	0	0.370917200867911	0	5	0	8	0	0	0	1	0
-BC029722	3.19971849117162	0.500786066092323	4.04549496806726	0.0442893889824016	0.0927232895943489	1.02178221965186	5	1.50564007410296	0	0.532561951711286	0	0	0	0	0	4	0	1	0	0	0	0	0
-D630024D03Rik	4.06980775023739	0.7082404013179	4.03667120501825	0.0445215586938516	0.0928700561145873	3.02593312554885	8	0	0	0	4.31711092832003	0	0	0	0	0	0	0	8	0	0	0	0
-0610040F04Rik	2.01747357743795	0.977371680002771	4.03475814713754	0.0445720636117494	0.0928700561145873	0.261267095275689	13	0.752820037051481	1.22515810725746	2.66280975855643	1.07927773208001	0.744902431617745	0	0.370917200867911	0	2	2	5	2	1	0	1	0
-Xist	4.05419301544091	0.707395597770275	4.030694429235	0.044679546414687	0.0928700561145873	3.00206353206658	8	0	0	4.26049561369029	0	0	0	0	0	0	0	8	0	0	0	0	0
-2810013P06Rik	2.06704188927478	0.967762003264331	4.03048600568275	0.0446850664390083	0.0928700561145873	0.309415407092519	13	1.50564007410296	2.45031621451491	1.06512390342257	0.539638866040004	0	0	0.741834401735823	0	4	4	2	1	0	0	2	0
-Gm10516	3.08232207628801	0.440940231955907	4.02405037505429	0.0448558657202631	0.0929488325352486	0.663213974166099	4	0.376410018525741	0.612579053628728	0	1.07927773208001	0	0	0	0	1	1	0	2	0	0	0	0
-Snord100	0.635613525765355	6.08912492232221	4.02292153684416	0.0448858954661893	0.0929488325352486	0.0868973476548087	1006	74.1527736495709	82.0855931862496	85.2099122738058	83.6440242362007	51.3982677816244	43.3106630929833	59.3467521388658	54.4014184199203	197	134	160	155	69	56	160	75
-Mir129-1	3.07872386541409	0.440724844947958	4.01695028567392	0.0450450973198572	0.0931095218151395	0.663220785699084	4	0.376410018525741	0.612579053628728	1.06512390342257	0	0	0	0	0	1	1	2	0	0	0	0	0
-Snora23	2.947659078747	1.00398627395562	4.01281950918959	0.0451555774466811	0.0931691028330256	1.19780792767109	14	3.01128014820593	0	2.66280975855643	0	0	0	0.370917200867911	0	8	0	5	0	0	0	1	0
-Mir294	3.06349997293662	0.439853358744087	3.9874899121061	0.0458393037569237	0.0936201232643365	0.663248346366127	4	0.376410018525741	0	0.532561951711286	1.07927773208001	0	0	0	0	1	0	1	2	0	0	0	0
-Snora70	3.06349997293662	0.439853358744087	3.9874899121061	0.0458393037569237	0.0936201232643365	0.663248346366127	4	0.376410018525741	0	0.532561951711286	1.07927773208001	0	0	0	0	1	0	1	2	0	0	0	0
-2010003O02Rik	1.98348239078603	1.15376056733645	3.98420904401608	0.0459286594553536	0.0936201232643365	0.398601895191753	17	1.12923005557722	1.22515810725746	3.19537171026772	1.61891659812001	0	0	1.11275160260373	0	3	2	6	3	0	0	3	0
-1700034P13Rik	3.06170605431538	0.439745726709386	3.98398051108368	0.045934890470963	0.0936201232643365	0.663251750248647	4	0.376410018525741	0	1.06512390342257	0.539638866040004	0	0	0	0	1	0	2	1	0	0	0	0
-Fam120aos	3.06170605431538	0.439745726709386	3.98398051108368	0.045934890470963	0.0936201232643365	0.663251750248647	4	0.376410018525741	0	1.06512390342257	0.539638866040004	0	0	0	0	1	0	2	1	0	0	0	0
-A730020M07Rik	3.05991259759458	0.439638100977263	3.98047511873451	0.0460305776961374	0.0936201232643365	0.66325515393893	4	0.376410018525741	0	1.59768585513386	0	0	0	0	0	1	0	3	0	0	0	0	0
-F630206G17Rik	3.05991259759458	0.439638100977263	3.98047511873451	0.0460305776961374	0.0936201232643365	0.66325515393893	4	0.376410018525741	0	1.59768585513386	0	0	0	0	0	1	0	3	0	0	0	0	0
-Gm21944	3.05991259759458	0.439638100977263	3.98047511873451	0.0460305776961374	0.0936201232643365	0.66325515393893	4	0.376410018525741	0	1.59768585513386	0	0	0	0	0	1	0	3	0	0	0	0	0
-Mir3470a	1.65480723982972	2.35026931926344	3.95738884280733	0.0466660382193545	0.0947436825770168	0.475481922306827	61	8.65743042609204	1.22515810725746	10.1186770825144	2.69819433020002	3.72451215808872	0.773404698088987	1.85458600433956	0.725352245598938	23	2	19	5	5	1	5	1
-Mir669e	2.01012761708276	0.976761579480109	3.93592654567248	0.0472650967414501	0.0957894766998127	0.278646788851163	13	0.752820037051481	0.612579053628728	2.13024780684514	2.15855546416002	0	0.773404698088987	0.370917200867911	0	2	1	4	4	0	1	1	0
-5730408K05Rik	3.03229149852466	0.437585811559422	3.92303751985238	0.0476287501010473	0.096355326002296	0.663320059641159	4	0.752820037051481	0.612579053628728	0	0.539638866040004	0	0	0	0	2	1	0	1	0	0	0	0
-Alg11	2.54969310547172	0.91195896231435	3.9125440107257	0.0479269953855071	0.0967870827165727	0.684211815681199	12	2.63487012968019	0	1.59768585513386	0.539638866040004	0	0	0	0.725352245598938	7	0	3	1	0	0	0	1
-BC031361	3.01357415843155	0.436500850557613	3.88761514649679	0.0486434507047088	0.0977412097808061	0.663354373887665	4	0.752820037051481	0	0.532561951711286	0.539638866040004	0	0	0	0	2	0	1	1	0	0	0	0
-1500015L24Rik	3.0117887696355	0.436393404882941	3.88421268494564	0.0487421107495869	0.0977412097808061	0.663357772138628	4	0.752820037051481	0	1.06512390342257	0	0	0	0	0	2	0	2	0	0	0	0	0
-Cyp2d37-ps	3.0117887696355	0.436393404882941	3.88421268494564	0.0487421107495869	0.0977412097808061	0.663357772138628	4	0.752820037051481	0	1.06512390342257	0	0	0	0	0	2	0	2	0	0	0	0	0
-Trpt1	3.0117887696355	0.436393404882941	3.88421268494564	0.0487421107495869	0.0977412097808061	0.663357772138628	4	0.752820037051481	0	1.06512390342257	0	0	0	0	0	2	0	2	0	0	0	0	0
-Mir297-2	1.54223903109748	2.09323284778587	3.86609307485566	0.0492710895725632	0.0986286196531484	0.370747786570236	47	4.14051020378315	3.67547432177237	8.52099122738058	2.15855546416002	3.72451215808872	0.773404698088987	1.11275160260373	0.725352245598938	11	6	16	4	5	1	3	1
-Snhg3	1.23410251082108	2.87013370923104	3.85237574901876	0.0496755800486956	0.099264162584171	0.271418782674104	94	10.5394805187207	3.67547432177237	9.58611513080315	9.71349958872008	6.7041218845597	1.54680939617797	3.70917200867911	2.17605673679681	28	6	18	18	9	2	10	3
-Jmjd4	2.1543240246942	1.07901960587324	3.84243987145646	0.0499707546357256	0.099679424893991	0.489459762198095	15	0.752820037051481	0.612579053628728	3.727933661979	1.61891659812001	0.744902431617745	0.773404698088987	0	0	2	1	7	3	1	1	0	0
-Mir465	2.98235832242489	0.434236891175304	3.82488269524673	0.0504968824968798	0.100553129020837	0.663425979375128	4	1.12923005557722	0.612579053628728	0	0	0	0	0	0	3	1	0	0	0	0	0	0
-D930015M05Rik	2.03574906278115	1.28114908660781	3.79290306775945	0.0514703053079524	0.102276182843222	0.5286307294293	20	2.25846011115444	0.612579053628728	4.79305756540158	0.539638866040004	0	0.773404698088987	0.370917200867911	0.725352245598938	6	1	9	1	0	1	1	1
-4930414N06Rik	2.96376667824731	0.433153838612419	3.7905905952123	0.0515414593644634	0.102276182843222	0.663460235997038	4	1.12923005557722	0	0.532561951711286	0	0	0	0	0	3	0	1	0	0	0	0	0
-Mirlet7f-2	0.586189945015586	9.80950112843876	3.7829242107611	0.0517780968044237	0.10256737578793	0.0860665007820653	14033	912.417884906396	1021.78186145272	1238.20653772874	1129.46414662173	555.697213986838	518.181147719621	1246.28179491618	541.838127462407	2424	1668	2325	2093	746	670	3360	747
-C920021L13Rik	1.76367634720298	1.70225824660072	3.77610677352993	0.0519894954270699	0.102807650402577	0.46617298721559	32	2.25846011115444	0.612579053628728	5.32561951711286	4.85674979436004	0	1.54680939617797	0.741834401735823	1.45070449119788	6	1	10	9	0	2	2	2
-Gm15417	1.67983957433172	1.80164992122508	3.71610398710266	0.0538899763171794	0.106305509612955	0.437532321965498	35	1.50564007410296	2.45031621451491	3.727933661979	7.01530525852006	1.48980486323549	2.32021409426696	0.741834401735823	0	4	4	7	13	2	3	2	0
-Mir411	-0.788462638146412	7.18678006636406	3.7126599791194	0.0540012681329112	0.106305509612955	0.155219066390438	2196	193.474749522231	123.740968833003	42.0723941851916	64.2170250587605	152.704998481638	174.789461768111	222.179403319879	182.788765890932	514	202	79	119	205	226	599	252
-Mir33	1.05704167432926	3.14606659666135	3.71152933168249	0.0540378576472513	0.106305509612955	0.207018017781761	118	13.5507606669267	9.80126485805965	5.32561951711286	11.8720550528801	2.97960972647098	6.18723758471189	6.30559241475449	3.62676122799469	36	16	10	22	4	8	17	5
-A630072M18Rik	1.68258239677861	1.28602336518056	3.70225210459996	0.0543390770575679	0.106516799810481	0.274903009044649	20	1.8820500926287	3.67547432177237	1.06512390342257	1.61891659812001	0.744902431617745	0	0.741834401735823	0.725352245598938	5	6	2	3	1	0	2	1
-4931403G20Rik	2.91589823742362	0.429919394234628	3.69960583714786	0.0544253236542598	0.106516799810481	0.663562545749751	4	1.50564007410296	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0
-Gm4265	2.91589823742362	0.429919394234628	3.69960583714786	0.0544253236542598	0.106516799810481	0.663562545749751	4	1.50564007410296	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0
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-Mir484	-0.63251033789946	7.18286805708198	3.67311765636983	0.0552966594113517	0.107670422228112	0.0998462982151122	2052	107.276855279836	137.217708012835	53.7887571228399	155.415993419521	199.633851673556	173.242652371933	156.527058766259	174.084538943745	285	224	101	288	268	224	422	240
-Mir3086	-1.59145486347128	1.07120757999586	3.67308122293966	0.0552978680330181	0.107670422228112	0.155363987763891	15	0.752820037051481	0	0.532561951711286	0.539638866040004	1.48980486323549	1.54680939617797	1.85458600433956	1.45070449119788	2	0	1	1	2	2	5	2
-Zfp410	2.40050624799357	1.27209510414984	3.66070721053791	0.055709981384655	0.108288055809014	0.882974817159639	20	3.76410018525741	0	3.19537171026772	1.07927773208001	0	1.54680939617797	0	0	10	0	6	2	0	2	0	0
-Snord71	0.812834481626158	4.57472241895141	3.65038540135801	0.056056238579516	0.108775796291204	0.14507715065225	341	35.0061317228939	31.2415317350651	13.8466107444934	34.5368874265603	14.8980486323549	15.4680939617797	14.0948536329806	21.0352151223692	93	51	26	64	20	20	38	29
-Snhg4	-1.23773296257918	2.10618734501935	3.63164358620883	0.056690804993097	0.109820387940787	0.232173331853763	47	2.63487012968019	1.83773716088618	1.59768585513386	1.61891659812001	2.97960972647098	4.64042818853392	4.08008920954702	7.25352245598938	7	3	3	3	4	6	11	10
-Mir5117	-0.918628727646429	3.53006698882797	3.61010751752031	0.0574294066806644	0.11106263224176	0.168816098395175	153	8.2810204075663	9.80126485805965	7.45586732395801	3.77747206228003	8.19392674779519	16.2414986598687	14.4657708338485	16.6831016487756	22	16	14	7	11	21	39	23
-A930005H10Rik	2.28834272089687	1.01956589864802	3.59998628180936	0.0577800479139781	0.111551666108036	0.713905461258199	14	1.12923005557722	1.83773716088618	0	3.23783319624003	0	0	0.741834401735823	0	3	3	0	6	0	0	2	0
-Mir29b-2	-1.44795171375512	1.94007043007237	3.59625074896648	0.0579100359845348	0.111613768679652	0.353810081928311	41	1.8820500926287	0	1.06512390342257	2.69819433020002	2.23470729485323	3.86702349044493	5.56375801301867	4.35211347359363	5	0	2	5	3	5	15	6
-Mir3069	2.21555843820049	0.756685666656939	3.56973150067031	0.0588418247566771	0.113218418292358	0.320229313843649	9	1.50564007410296	0	1.06512390342257	1.07927773208001	0.744902431617745	0	0	0	4	0	2	2	1	0	0	0
-Gm12359	2.16898632974045	1.4882686924078	3.56048941623669	0.0591702906624582	0.11365875697957	0.838744382534598	26	3.38769016673167	0	5.85818146882415	1.07927773208001	0.744902431617745	0	1.11275160260373	0	9	0	11	2	1	0	3	0
-4930512B01Rik	2.31169575445299	0.751907182201018	3.55318077662759	0.0594314215560064	0.113968490748577	0.447887175675507	9	1.50564007410296	0.612579053628728	1.59768585513386	0	0	0	0.370917200867911	0	4	1	3	0	0	0	1	0
-9330175M20Rik	-1.83913038229393	0.769181445189637	3.53330459070706	0.0601477967137221	0.115148718205297	0.12349436152705	9	0.376410018525741	0	0	0.539638866040004	1.48980486323549	1.54680939617797	0.741834401735823	0.725352245598938	1	0	0	1	2	2	2	1
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-Gm7854	1.8130525534441	1.40076095337658	3.51463717551188	0.0608289743711412	0.116063310631224	0.460693165702335	23	3.01128014820593	4.2880533754011	0.532561951711286	1.61891659812001	0.744902431617745	1.54680939617797	0.370917200867911	0	8	7	1	3	1	2	1	0
-Snord15a	1.26556615125299	2.28978783966135	3.51074803839542	0.0609719203238878	0.116141838212948	0.266691310482541	57	7.52820037051481	6.12579053628728	4.79305756540158	2.15855546416002	2.97960972647098	2.32021409426696	1.85458600433956	1.45070449119788	20	10	9	4	4	3	5	2
-A330023F24Rik	-0.578411379373374	8.69459977720854	3.50754760363478	0.0610898210635382	0.116172476389162	0.0896883067913636	6103	408.781280118954	382.861908517955	135.803297686378	398.793122003563	490.890702436094	450.894938985879	549.699291686245	488.887413533684	1086	625	255	739	659	583	1482	674
-Wdr13	-1.72012346832078	0.929108611192646	3.4992517065301	0.0613965647109117	0.116561531339684	0.196132662445652	12	0.752820037051481	0	0.532561951711286	0	1.48980486323549	0.773404698088987	1.11275160260373	2.17605673679681	2	0	1	0	2	1	3	3
-2010310C07Rik	2.19594941926096	0.754516632646807	3.46141482333363	0.0628165440985541	0.119059263814701	0.339304015130962	9	1.8820500926287	0.612579053628728	0.532561951711286	0.539638866040004	0.744902431617745	0	0	0	5	1	1	1	1	0	0	0
-0610009L18Rik	-1.70953095047412	1.30558372556489	3.43327300907768	0.0638953546806545	0.120828775476832	0.42773835425411	21	1.12923005557722	0	0.532561951711286	0.539638866040004	1.48980486323549	1.54680939617797	4.08008920954702	0.725352245598938	3	0	1	1	2	2	11	1
-Mir29c	-0.579909849202081	8.6801221089121	3.43155254242405	0.0639619460017588	0.120828775476832	0.0921705197821209	6038	403.88794987812	382.249329464326	130.477678169265	395.555288807323	487.911092709623	447.027915495434	542.651864869754	483.809947814491	1073	624	245	733	655	578	1463	667
-9530026P05Rik	-1.7605961243528	1.31005038813491	3.41337008384323	0.0646702474343339	0.121964879872025	0.474959668640273	20	0	0.612579053628728	2.13024780684514	0	2.23470729485323	3.09361879235595	1.48366880347165	2.90140898239575	0	1	4	0	3	4	4	4
-Ranbp3	1.94585296479219	1.31602180536296	3.39704286178514	0.0653134113579484	0.122974591352177	0.559883347902341	21	3.76410018525741	1.22515810725746	2.66280975855643	0.539638866040004	0	1.54680939617797	0	0.725352245598938	10	2	5	1	0	2	0	1
-Snora26	1.86839512049783	0.97078207300884	3.34850128624277	0.0672662307499137	0.126442783007663	0.296473421144447	13	2.25846011115444	1.22515810725746	0.532561951711286	1.07927773208001	0	0.773404698088987	0	0.725352245598938	6	2	1	2	0	1	0	1
-Gm5089	2.28406661080148	1.75471782411861	3.34448803344576	0.0674304520811639	0.126543003001	1.08109229776954	34	3.76410018525741	0	10.1186770825144	0.539638866040004	0.744902431617745	0.773404698088987	0	1.45070449119788	10	0	19	1	1	1	0	2
-9430008C03Rik	1.89674596190813	1.50713232824516	3.33238403629771	0.0679283455311257	0.127268049673258	0.617315662879925	26	3.01128014820593	0.612579053628728	5.32561951711286	1.61891659812001	1.48980486323549	0	0	1.45070449119788	8	1	10	3	2	0	0	2
-Snora28	1.14967422700679	2.54114084010672	3.32568385981009	0.0682056437241508	0.127578097523371	0.243892218992173	71	9.41025046314352	4.2880533754011	6.92330537224672	4.31711092832003	2.23470729485323	3.86702349044493	1.85458600433956	3.62676122799469	25	7	13	8	3	5	5	5
-3110045C21Rik	1.74505885736988	1.30320211999434	3.32083349079693	0.0684071397663212	0.127745575242836	0.429780317265908	21	3.76410018525741	1.83773716088618	1.06512390342257	1.07927773208001	0	0	1.11275160260373	0.725352245598938	10	3	2	2	0	0	3	1
-5730422E09Rik	2.17813007132659	0.69991420705385	3.31793277917728	0.0685279464912759	0.127762070174094	0.327848806594992	8	0.752820037051481	1.22515810725746	1.59768585513386	0	0	0	0.370917200867911	0	2	2	3	0	0	0	1	0
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-Mirlet7f-1	-0.618847205874743	5.7539252385751	3.28552344457632	0.0698933383674589	0.129461524476089	0.100580078513029	779	40.2758719822543	47.7811661830408	42.0723941851916	37.2350817567603	72.2555358669212	57.231947658585	76.0380261779218	50.7746571919256	107	78	79	69	97	74	205	70
-BC090627	-1.38077885406166	2.12933903001116	3.26984269690561	0.0705643895088469	0.130492655477462	0.38779446564614	47	2.63487012968019	0.612579053628728	1.06512390342257	3.23783319624003	2.97960972647098	9.28085637706784	2.22550320520747	6.52817021039044	7	1	2	6	4	12	6	9
-Ldha	1.41519140662907	1.99546173390349	3.24154661229641	0.0717928362676978	0.132549556927902	0.366966029358505	43	3.38769016673167	1.22515810725746	6.39074342053543	5.39638866040004	0.744902431617745	3.09361879235595	1.48366880347165	0.725352245598938	9	2	12	10	1	4	4	1
-Snord55	0.573286347206465	7.06540834889277	3.23258794246729	0.0721865297249036	0.133061115373368	0.0928136803605377	2070	173.901428558892	189.286927571277	135.803297686378	134.909716510001	92.3679015206004	78.1138745069877	166.91274039056	86.3169172262736	462	309	255	250	124	101	450	119
-Rmst	-2.2719524655272	0.840227711282082	3.20385953341656	0.0734647104225492	0.135198765471175	0.855385796986242	10	0.376410018525741	0	0.532561951711286	0	0.744902431617745	3.86702349044493	0	1.45070449119788	1	0	1	0	1	5	0	2
-Gm10804	1.94827721953342	0.916648370305759	3.19714358228513	0.0737670039720425	0.135536475897102	0.41514500422894	12	1.12923005557722	0.612579053628728	2.66280975855643	0.539638866040004	0	0	0.741834401735823	0	3	1	5	1	0	0	2	0
-9330162012Rik	2.29431770590357	0.808162714550698	3.19178997460511	0.0740089330230366	0.135762367490811	0.637228874009436	10	2.25846011115444	0.612579053628728	1.06512390342257	0	0	0	0	0.725352245598938	6	1	2	0	0	0	0	1
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-Gm16833	1.63703920992267	1.06403583359424	3.1800408757336	0.0745428650347607	0.136303540071574	0.231429707144515	15	1.50564007410296	0.612579053628728	2.13024780684514	1.61891659812001	0	0	0.741834401735823	0.725352245598938	4	1	4	3	0	0	2	1
-2610020C07Rik	2.37381043050929	1.23920884168522	3.16793680836009	0.0750972571670351	0.137097552684139	1.07912563436834	19	2.63487012968019	0	4.79305756540158	0.539638866040004	1.48980486323549	0	0	0	7	0	9	1	2	0	0	0
-9330179D12Rik	-1.44454904349032	1.96602595763002	3.1568170110455	0.0756104726879749	0.137813976576644	0.428251678718882	40	0	1.83773716088618	1.59768585513386	3.23783319624003	4.46941458970647	4.64042818853392	2.59642040607538	6.52817021039044	0	3	3	6	6	6	7	9
-Cops5	2.42493991988414	1.18865263844183	3.15052049493848	0.0759027480624063	0.138126053491556	1.15615398282634	18	3.01128014820593	0	4.26049561369029	0	0.744902431617745	0	0.370917200867911	0	8	0	8	0	1	0	1	0
-Snord17	0.688186198794369	6.53903318264474	3.12589464667987	0.0770575636678555	0.140004267746852	0.137600334299236	1360	122.709666039391	139.66802422735	45.2677658954593	145.162854964761	86.4086820676584	60.325566450941	54.8957457284509	79.7887470158832	326	228	85	269	116	78	148	110
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-4930455H04Rik	2.21756582368465	0.760890915501029	3.07775090257693	0.0793702125246859	0.143293374194093	0.552609695738945	9	1.12923005557722	0.612579053628728	2.13024780684514	0	0	0.773404698088987	0	0	3	1	4	0	0	1	0	0
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-Mir22hg	-0.749289612870416	16.8472649773795	3.0628396082966	0.0801015724741567	0.144085810733476	0.174189748040419	1751491	99685.7944362275	109054.998601308	38034.5094673166	105050.958413142	149598.01043936	121838.309113449	184499.779469712	135471.137501531	264833	178026	71418	194669	200829	157535	497415	186766
-Elmo1	-2.07301354747071	0.582197696716647	3.06108750847979	0.08018798406289	0.144085810733476	0.264664941303461	6	0	0	0	0.539638866040004	0.744902431617745	1.54680939617797	0.741834401735823	0	0	0	0	1	1	2	2	0
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-Mir671	0.575013951814249	6.0570537328933	2.94061465563659	0.0863778579593577	0.153515788055494	0.0983236860031686	973	63.6132931308502	96.1749114197103	72.9609873844462	80.4061910399606	61.8269018242728	47.1776865834282	59.7176693397337	40.6197257535405	169	157	137	149	83	61	161	56
-Gm10125	-2.1452800616706	0.587862989606023	2.93442430264794	0.086709569975526	0.153865659941019	0.451500784124522	6	0	0	0.532561951711286	0	1.48980486323549	1.54680939617797	0.370917200867911	0	0	0	1	0	2	2	1	0
-2010009K17Rik	1.96055287319474	1.32277568387187	2.91082001033933	0.0879871276255113	0.155890236988678	0.761558387662271	21	2.63487012968019	0	4.26049561369029	1.61891659812001	1.48980486323549	0.773404698088987	0	0	7	0	8	3	2	1	0	0
-2900056M20Rik	-1.91775076130403	0.820613808625248	2.90416460447901	0.0883510190324529	0.15607547835418	0.499923546279751	10	0	0	0	1.07927773208001	1.48980486323549	1.54680939617797	1.48366880347165	0	0	0	0	2	2	2	4	0
-Mir1981	0.73767827965099	4.38081005733277	2.90390479032837	0.0883652576834357	0.15607547835418	0.147754252443895	295	30.489211500585	25.7283202524066	12.2489248893596	29.1404987661602	20.1123656536791	13.9212845656018	11.8693504277732	13.0563404207809	81	42	23	54	27	18	32	18
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-Mir1955	1.88384801300483	0.639671826801534	2.7777503845375	0.0955823395615566	0.165743844133338	0.117361646904145	7	1.12923005557722	0.612579053628728	0.532561951711286	0.539638866040004	0.744902431617745	0	0	0	3	1	1	1	1	0	0	0
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-Oxsr1	1.80409098647694	1.42731195989163	2.74522997923213	0.0975450418164591	0.168125215577915	0.711453031745412	24	3.38769016673167	0	5.32561951711286	0.539638866040004	0.744902431617745	0.773404698088987	0.370917200867911	0.725352245598938	9	0	10	1	1	1	1	1
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-4930413G21Rik	1.95835690949541	0.930379450543939	2.61922175978353	0.105576209115354	0.179649569155885	0.697287105591242	12	0.752820037051481	3.67547432177237	1.06512390342257	0	0.744902431617745	0	0.370917200867911	0	2	6	2	0	1	0	1	0
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-Dancr	1.37718408759755	2.08329778707713	2.5408962339772	0.110931803168658	0.186961872105522	0.509160732892771	48	7.52820037051481	1.22515810725746	6.39074342053543	1.61891659812001	0	1.54680939617797	1.85458600433956	2.90140898239575	20	2	12	3	0	2	5	4
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-Afg3l1	1.48878907990838	1.53298802047544	2.25597647981274	0.133099474807165	0.218512950726584	0.605022791019069	27	2.63487012968019	0	5.32561951711286	2.15855546416002	0	1.54680939617797	1.11275160260373	0.725352245598938	7	0	10	4	0	2	3	1
-1110054M08Rik	1.62607709394344	1.10846820178379	2.23883777740752	0.134582102712517	0.2203627896505	0.586825375590218	16	2.25846011115444	0	3.19537171026772	0.539638866040004	0.744902431617745	0	0.370917200867911	0.725352245598938	6	0	6	1	1	0	1	1
-Gabpb1	1.8877934744052	0.644895200393036	2.2384885870073	0.134612501653286	0.2203627896505	0.466643761334106	7	0.376410018525741	0	1.59768585513386	1.07927773208001	0	0	0	0.725352245598938	1	0	3	2	0	0	0	1
-1810062O18Rik	1.90655347492814	0.646997412885778	2.21392366604849	0.136770420295042	0.223574569565391	0.519639812465789	7	0.376410018525741	1.22515810725746	1.59768585513386	0	0.744902431617745	0	0	0	1	2	3	0	1	0	0	0
-Rnu73b	1.1294430209651	2.00334001585587	2.20989050653489	0.137128403530578	0.223839067851773	0.342987267601879	44	6.77538033346333	1.22515810725746	4.26049561369029	2.69819433020002	1.48980486323549	2.32021409426696	1.11275160260373	2.17605673679681	18	2	8	5	2	3	3	3
-Mir485	-1.61130823956714	0.965437135424848	2.17449464502602	0.14031560127479	0.228479477566918	0.595115069085034	13	0.376410018525741	1.22515810725746	0	0	0.744902431617745	0	2.59642040607538	1.45070449119788	1	2	0	0	1	0	7	2
-Mir299	-0.985886212461878	1.99934376192861	2.17387969790019	0.140371703570911	0.228479477566918	0.247192543396564	43	2.63487012968019	2.45031621451491	1.06512390342257	1.61891659812001	5.21431702132421	3.86702349044493	4.45100641041494	2.17605673679681	7	4	2	3	7	5	12	3
-Zfp326	1.42800580995752	1.2389494049915	2.16911986522787	0.140806801416007	0.228861197173311	0.441869400453599	19	2.63487012968019	0	2.13024780684514	2.15855546416002	1.48980486323549	0.773404698088987	0.370917200867911	0	7	0	4	4	2	1	1	0
-Vaultrc5	-0.439038195253229	7.1589713812088	2.15762491942541	0.141863819797126	0.230251235261054	0.0814636368813792	2022	91.467634501755	97.4000695269678	139.531231348357	154.336715687441	192.184827357378	124.518156392327	142.06128793241	195.845106311713	243	159	262	286	258	161	383	270
-Kat5	1.82250028311509	0.936987866235069	2.13330396743077	0.144129795274976	0.233596727853335	0.804256971018256	12	0.376410018525741	2.45031621451491	2.66280975855643	0	0	0.773404698088987	0	0.725352245598938	1	4	5	0	0	1	0	1
-Mir676	-0.446802845867355	6.53242393015933	2.11909507519026	0.145472474586545	0.23543843050106	0.0840718828554176	1363	70.7650834828393	83.310751293507	76.1563590947139	79.8665521739206	108.755755016191	77.3404698088987	135.01386111592	100.098609892653	188	136	143	148	146	100	364	138
-D130009I18Rik	1.81913658193294	1.05660008926899	2.1004873208015	0.147252200246514	0.237981247140612	0.969130775042379	15	2.25846011115444	3.06289526814364	0.532561951711286	0	0	0	1.11275160260373	0	6	5	1	0	0	0	3	0
-4930471I20Rik	2.00255834299285	0.971879491293969	2.08654608279147	0.148601704127711	0.239822552206108	1.19610967428711	13	1.12923005557722	0	4.26049561369029	0	0	0	0.370917200867911	0.725352245598938	3	0	8	0	0	0	1	1
-Nkx6-2	-1.80867083405477	0.51905820233254	2.07067242350126	0.150155304998473	0.241987574863358	0.378967851586558	5	0	0.612579053628728	0	0	0.744902431617745	1.54680939617797	0.370917200867911	0	0	1	0	0	1	2	1	0
-2810008D09Rik	0.992275793227007	3.31325368484776	2.05928786482749	0.151280855928879	0.243457625690904	0.384912015572497	137	21.831781074493	2.45031621451491	16.5094205030499	3.77747206228003	6.7041218845597	3.09361879235595	4.82192361128285	7.97887470158832	58	4	31	7	9	4	13	11
-Adam17	1.29736312070878	1.35888681515096	2.05399049164013	0.151807841106095	0.243736199619237	0.389874918889613	22	3.01128014820593	0.612579053628728	2.66280975855643	1.61891659812001	0	1.54680939617797	0.370917200867911	1.45070449119788	8	1	5	3	0	2	1	2
-4932702P03Rik	1.88393800726103	1.28729255558247	2.05325482165607	0.151881190122066	0.243736199619237	1.16513146848805	20	2.25846011115444	1.22515810725746	4.79305756540158	0	2.23470729485323	0	0	0	6	2	9	0	3	0	0	0
-Mir26b	0.381406457171917	11.5945020692124	2.04699250556749	0.152507193679534	0.244397061781388	0.0679015281500295	46666	3701.99253220066	4096.3161316153	2404.51721197646	3786.64592300271	2674.94463193932	2413.02265803764	3120.52641090174	2530.0286326491	9835	6687	4515	7017	3591	3120	8413	3488
-Flcn	1.46960323620757	1.35192910254652	2.04233191077918	0.152974980663752	0.244802879295008	0.62145815149932	22	2.63487012968019	1.22515810725746	4.26049561369029	0	0	0.773404698088987	1.11275160260373	0.725352245598938	7	2	8	0	0	1	3	1
-Trpc4	-1.74596825626093	0.71317759283185	2.03938581517844	0.153271520914362	0.24493390106903	0.663998693170247	8	0.376410018525741	0	0	0.539638866040004	2.97960972647098	0.773404698088987	0.370917200867911	0	1	0	0	1	4	1	1	0
-2610203C22Rik	1.96678109286618	1.0656769981979	2.03321408643026	0.153894853126812	0.245586052332437	1.20264987743188	15	2.25846011115444	0	3.727933661979	0	0.744902431617745	0.773404698088987	0	0	6	0	7	0	1	1	0	0
-Mir223	-0.528641311341049	6.02781187693563	2.01628240521794	0.155619736218572	0.24799178634831	0.123647105305382	928	44.7927922045631	63.095642523759	28.2257834406982	75.0098023795606	73.000438298539	84.3011120916996	79.376280985733	67.4577588407012	119	103	53	139	98	109	214	93
-F630028O10Rik	-0.528638261243246	6.02781187693563	2.0138952875032	0.155864679701581	0.248035703681316	0.123802876861573	928	44.7927922045631	63.095642523759	28.2257834406982	75.0098023795606	73.000438298539	84.3011120916996	79.376280985733	67.4577588407012	119	103	53	139	98	109	214	93
-Mir103-2	0.785120714479361	2.71893553817616	2.01013243683963	0.156251677487728	0.248305242358632	0.185923137316202	81	6.39897031493759	6.12579053628728	6.92330537224672	8.09458299060006	5.21431702132421	4.64042818853392	3.3382548078112	2.90140898239575	17	10	13	15	7	6	9	4
-1500011K16Rik	2.11413372855866	0.642522158922088	2.00221088137035	0.157069958786553	0.249258446419272	1.18295805516084	7	0	0	2.13024780684514	1.07927773208001	0	0	0.370917200867911	0	0	0	4	2	0	0	1	0
-Mir5128	1.61359485230055	1.2738493521877	1.99369517324101	0.157955052207268	0.250314881345129	0.813074408757041	20	2.63487012968019	0	4.26049561369029	0.539638866040004	0	0	0.741834401735823	1.45070449119788	7	0	8	1	0	0	2	2
-Mphosph9	1.79236689198879	0.636333411267628	1.98570828328981	0.158790340384575	0.251289567793065	0.508944007080253	7	1.50564007410296	0.612579053628728	0	0.539638866040004	0	0	0	0.725352245598938	4	1	0	1	0	0	0	1
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-4930417O13Rik	1.71715010444169	0.926786533466471	1.97702501279526	0.159704166608603	0.252036589350507	0.743832722550382	12	1.12923005557722	0	2.66280975855643	1.07927773208001	1.48980486323549	0	0	0	3	0	5	2	2	0	0	0
-Gm14872	1.93209082136728	0.649147101892238	1.9603455254205	0.161476369969484	0.254481406264063	0.816935547976011	7	0.376410018525741	2.45031621451491	0.532561951711286	0	0.744902431617745	0	0	0	1	4	1	0	1	0	0	0
-Mir3087	-1.63929497611101	0.718224595257031	1.95615044185889	0.161925620826439	0.254532254454282	0.535428871476493	8	0	1.22515810725746	0	0	2.23470729485323	0.773404698088987	0.370917200867911	0.725352245598938	0	2	0	0	3	1	1	1
-Dlg1	1.19604003304172	2.0318454145106	1.9558785095741	0.161954791177746	0.254532254454282	0.500980604511908	45	4.14051020378315	0.612579053628728	9.58611513080315	1.61891659812001	1.48980486323549	1.54680939617797	2.22550320520747	1.45070449119788	11	1	18	3	2	2	6	2
-Mir154	-1.46711327280048	1.20680226810302	1.95174359983792	0.162399085082763	0.254879444400871	0.655814506748708	18	0.752820037051481	1.83773716088618	0	0	1.48980486323549	0	2.22550320520747	3.62676122799469	2	3	0	0	2	0	6	5
-Mir3060	-1.2113586950711	1.23412841117325	1.93404840964081	0.164316208256188	0.257328757236931	0.342800597958089	19	1.12923005557722	0.612579053628728	0	1.07927773208001	0.744902431617745	0.773404698088987	2.96733760694329	2.17605673679681	3	1	0	2	1	1	8	3
-4930599N23Rik	2.03468754035394	1.36669597820702	1.93318190516873	0.164410748488802	0.257328757236931	1.574325401684	22	1.8820500926287	0	7.45586732395801	0	0	0.773404698088987	0	1.45070449119788	5	0	14	0	0	1	0	2
-C130046K22Rik	-1.82497997235467	0.998221956150761	1.90372750409198	0.16766168551416	0.26205751119405	1.16292533112955	13	0	1.83773716088618	0	0	3.72451215808872	2.32021409426696	0.741834401735823	0	0	3	0	0	5	3	2	0
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-Snord15b	0.634264424966416	3.97493859739106	1.82067308272488	0.177233178762163	0.274014982340959	0.170515835029383	219	23.7138311671217	14.7018972870895	13.3140487927822	18.3477214453601	19.3674632220614	12.3744751694238	8.90201282082987	5.07746571919256	63	24	25	34	26	16	24	7
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-Snord58b	-0.959891864806359	4.98142254057752	1.77051212306474	0.183318712476616	0.281895755978193	0.473263658453828	394	17.3148608521841	26.953478359664	15.4442965996273	26.4423044359602	63.3167066875083	62.6457805452079	1.11275160260373	41.3450779991395	46	44	29	49	85	81	3	57
-Gm16845	1.16526727898085	1.63063614891485	1.76110091129479	0.184487257044476	0.28331084830114	0.45443580543518	30	3.01128014820593	1.22515810725746	3.19537171026772	3.23783319624003	0	3.09361879235595	1.48366880347165	0	8	2	6	6	0	4	4	0
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-Mir1843b	0.389851350480043	6.8875736230068	1.74809463046232	0.186116443251731	0.285045452013725	0.0783163506901775	1740	102.383525039001	120.065494511231	178.408253823281	131.132244447721	110.245559879426	84.3011120916996	111.275160260373	99.3732576470545	272	196	335	243	148	109	300	137
-Brd2	1.00128525429007	2.18480127537997	1.73149429279408	0.188220175014745	0.287880991544	0.385373147795245	52	5.64615027788611	1.22515810725746	5.32561951711286	5.39638866040004	2.97960972647098	3.09361879235595	2.59642040607538	0	15	2	10	10	4	4	7	0
-4930509E16Rik	1.75126346079811	0.87017516287105	1.72215197541634	0.189416274005641	0.289322581847974	1.02178786169832	11	1.50564007410296	3.06289526814364	0	0	0	0	0.370917200867911	0.725352245598938	4	5	0	0	0	0	1	1
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-Dnm1l	1.80630973357152	1.49903122302948	1.71111376342148	0.190840929140441	0.290720293924223	1.46946215427623	26	2.25846011115444	0	7.98842927566929	0	0	1.54680939617797	1.11275160260373	0	6	0	15	0	0	2	3	0
-Snora69	1.08869295668112	1.71806156711187	1.70101780588851	0.192154924081701	0.292331691169627	0.418293401276377	33	2.25846011115444	2.45031621451491	5.32561951711286	1.61891659812001	0.744902431617745	0	2.59642040607538	1.45070449119788	6	4	10	3	1	0	7	2
-E130317F20Rik	1.36400541731017	0.758279590034866	1.69878193542161	0.192447350456789	0.292386720201327	0.231002884653815	9	1.12923005557722	1.22515810725746	1.06512390342257	0	0	0	0.370917200867911	0.725352245598938	3	2	2	0	0	0	1	1
-A330032B11Rik	1.39818933903737	0.748748186748486	1.69255362514394	0.193264686981905	0.292951835102097	0.291687482395929	9	1.50564007410296	0.612579053628728	0.532561951711286	0.539638866040004	0	0	0.741834401735823	0	4	1	1	1	0	0	2	0
-9330178D15Rik	-1.98679676261055	0.524020298165048	1.69203592951643	0.193332806162909	0.292951835102097	1.3205532007011	5	0	0	0.532561951711286	0	0.744902431617745	2.32021409426696	0	0	0	0	1	0	1	3	0	0
-4930573O16Rik	1.59328290275501	0.573882656582763	1.68701795298712	0.193994535494436	0.293306722496002	0.314421647995105	6	1.12923005557722	0	0.532561951711286	0.539638866040004	0	0	0	0.725352245598938	3	0	1	1	0	0	0	1
-Chpt1	1.47700523685698	2.34168158861338	1.68501920720582	0.194258850745948	0.293306722496002	1.06784086774825	61	8.2810204075663	0	13.3140487927822	0	0.744902431617745	2.32021409426696	2.96733760694329	1.45070449119788	22	0	25	0	1	3	8	2
-Adamts10	1.92767141679506	0.821256886501406	1.68441981703105	0.194338196500418	0.293306722496002	1.44950467480606	10	0	2.45031621451491	2.13024780684514	0	0	0	0.741834401735823	0	0	4	4	0	0	0	2	0
-C030016D13Rik	1.59399520847019	0.575124507193501	1.64696610323885	0.199372364162675	0.300507090501469	0.358787781200008	6	1.12923005557722	0.612579053628728	0	0.539638866040004	0.744902431617745	0	0	0	3	1	0	1	1	0	0	0
-Gm12238	1.17743427197619	1.70057102419889	1.63788297384798	0.20061618016513	0.301982930829042	0.53847645030781	32	3.38769016673167	2.45031621451491	5.85818146882415	0	1.48980486323549	1.54680939617797	0.741834401735823	1.45070449119788	9	4	11	0	2	2	2	2
-Snord57	0.270666655755215	9.42386361558089	1.62967609542948	0.201747854955477	0.303286301059551	0.0422885257734828	10268	653.824202179212	827.594301452412	769.552020222808	749.018746063526	584.74840881993	575.413095378206	753.332834962728	570.852217286364	1737	1351	1445	1388	785	744	2031	787
-Pnpla2	1.09889328874293	1.70024363448059	1.61741482920614	0.203452629826889	0.305177539894076	0.44283962967608	32	3.76410018525741	0.612579053628728	4.26049561369029	2.69819433020002	2.97960972647098	0.773404698088987	0.370917200867911	1.45070449119788	10	1	8	5	4	1	1	2
-St5	1.14540632239041	1.43909936145621	1.61678363033081	0.203540848255383	0.305177539894076	0.427462889995435	24	2.63487012968019	1.22515810725746	3.727933661979	1.07927773208001	2.23470729485323	0	0.370917200867911	1.45070449119788	7	2	7	2	3	0	1	2
-D930016D06Rik	1.76685587915284	0.638496128878626	1.61355758338489	0.203992435707554	0.305453240344251	0.88787067352823	7	1.12923005557722	0	1.59768585513386	0	0.744902431617745	0	0	0	3	0	3	0	1	0	0	0
-Brat1	1.63806716830811	0.580282133402032	1.61096896164639	0.204355649440744	0.30559606292515	0.498016793789726	6	0.376410018525741	0	1.59768585513386	0.539638866040004	0	0	0	0.725352245598938	1	0	3	1	0	0	0	1
-Malat1	0.892035948894325	5.26274681035236	1.60518554190673	0.205169889192662	0.306412098912077	0.452900589946088	560	62.8604730937987	5.51321148265855	107.044952293969	16.7288048472401	26.8164875382388	31.7095926216485	9.27293002169778	36.2676122799469	167	9	201	31	36	41	25	50
-Snord73a	0.938581903974755	2.39902888782473	1.60119403868515	0.205734080105843	0.30685305281146	0.385824614925772	64	10.9158905372465	3.67547432177237	4.79305756540158	1.07927773208001	2.23470729485323	2.32021409426696	2.59642040607538	3.62676122799469	29	6	9	2	3	3	7	5
-Gm11602	1.10178148053282	2.35647563869741	1.59591013637908	0.206483768359912	0.307569164097466	0.576530554129637	61	8.2810204075663	1.83773716088618	9.58611513080315	1.07927773208001	0	3.09361879235595	2.22550320520747	4.35211347359363	22	3	18	2	0	4	6	6
-Pradc1	1.91674740534921	0.650415606184684	1.57297890760317	0.209774930983937	0.312044255071644	1.33002709755017	7	0	1.22515810725746	2.13024780684514	0	0	0.773404698088987	0	0	0	2	4	0	0	1	0	0
-Snord89	0.966574824460612	1.80434757594844	1.57118472472807	0.210035046358477	0.312044255071644	0.331669301499213	36	4.89333024083463	1.22515810725746	4.26049561369029	1.61891659812001	1.48980486323549	1.54680939617797	1.11275160260373	2.17605673679681	13	2	8	3	2	2	3	3
-Kcnq1ot1	1.4690186697538	1.11073986368061	1.55307986961569	0.212681344061251	0.315564907118189	0.811842989993509	16	2.63487012968019	0	2.66280975855643	0.539638866040004	0.744902431617745	0	0	1.45070449119788	7	0	5	1	1	0	0	2
-Mir879	-0.957422875609432	1.24255605117401	1.52112435477467	0.217449424119999	0.322220510286907	0.1980926097388	19	1.12923005557722	0.612579053628728	1.06512390342257	0.539638866040004	2.23470729485323	0.773404698088987	2.22550320520747	1.45070449119788	3	1	2	1	3	1	6	2
-Lrrc57	1.8847676489433	0.578218702340393	1.51434667879481	0.218477017960122	0.323323317110894	1.28595199102621	6	0	0	0.532561951711286	2.15855546416002	0	0	0.370917200867911	0	0	0	1	4	0	0	1	0
-A630010A05Rik	-1.06389667985724	1.44453280447873	1.49582214729094	0.22131531349231	0.327099446495759	0.426267937473902	24	1.8820500926287	0.612579053628728	0	1.61891659812001	1.48980486323549	4.64042818853392	1.85458600433956	1.45070449119788	5	1	0	3	2	6	5	2
-BC039771	1.70841256711362	0.635554931729437	1.49045673551048	0.222145608277726	0.327492386724679	0.929498731793523	7	1.50564007410296	0	1.06512390342257	0	0	0.773404698088987	0	0	4	0	2	0	0	1	0	0
-Snhg6	0.363253836487354	6.93079477897274	1.49039475718623	0.222155221143647	0.327492386724679	0.0798920539070874	1762	146.799907225039	144.56865665638	136.335859638089	116.022356198601	108.010852584573	106.72984833628	70.8451853657711	138.542278909397	390	236	256	215	145	138	191	191
-Mir199a-1	1.05557681067524	1.20418398339966	1.48741804710113	0.22261749692031	0.327750405143321	0.279838591324049	18	1.50564007410296	1.22515810725746	2.13024780684514	1.61891659812001	2.23470729485323	0	0.741834401735823	0	4	2	4	3	3	0	2	0
-Mir196b	-1.32127454614676	0.829618781393242	1.48196744206585	0.223466951282694	0.328281650450165	0.492761700442628	10	0	0.612579053628728	0	1.07927773208001	1.48980486323549	0	0.741834401735823	2.17605673679681	0	1	0	2	2	0	2	3
-Pex11b	1.65995741405808	0.804639894669543	1.47905581672054	0.223922306977752	0.328281650450165	1.10073827773407	10	1.50564007410296	0	2.13024780684514	0	0	0	0.741834401735823	0	4	0	4	0	0	0	2	0
-Mir15b	-0.394788504231884	6.20734639920343	1.47879336116712	0.223963407602626	0.328281650450165	0.0932309162192091	1064	61.3548330196957	61.8704844165015	46.3328897988819	82.5647465041206	90.1331942257471	75.0202557146317	85.6818734004875	80.5140992614821	163	101	87	153	121	97	231	111
-Uqcc	1.33988788764212	1.20237271081473	1.47773531358743	0.224129189921717	0.328281650450165	0.713263179339961	18	1.8820500926287	0	4.26049561369029	0.539638866040004	0	1.54680939617797	0.370917200867911	0.725352245598938	5	0	8	1	0	2	1	1
-Snord87	0.361531400618155	6.92853158846234	1.47349079410599	0.22479573166607	0.328835807475623	0.0800479606361491	1759	146.799907225039	143.956077602751	135.803297686378	116.022356198601	108.010852584573	106.72984833628	70.4742681649032	138.542278909397	390	235	255	215	145	138	190	191
-Parp6	1.31909232213893	1.41955838570186	1.46960937555209	0.225407335548571	0.32930828407288	0.794694003083279	24	3.01128014820593	0	4.26049561369029	1.07927773208001	0	1.54680939617797	1.48366880347165	0	8	0	8	2	0	2	4	0
-9130221H12Rik	1.81174070735099	0.574594586237392	1.46729529556962	0.225772920425449	0.329420591055547	1.1662362903797	6	0.376410018525741	0	2.13024780684514	0	0	0	0.370917200867911	0	1	0	4	0	0	0	1	0
-Mir381	-0.535423138275991	4.2010882103495	1.44983721333272	0.228554074799306	0.332839187589807	0.158316469762884	263	22.5846011115444	12.2515810725746	12.7814868410709	8.09458299060006	20.8572680852969	20.8819268484026	26.3351212616217	13.0563404207809	60	20	24	15	28	27	71	18
-Snora21	0.977714238380411	1.28903949414256	1.44893250051556	0.228699319080113	0.332839187589807	0.238819239186347	20	1.12923005557722	2.45031621451491	2.13024780684514	1.61891659812001	1.48980486323549	0	1.11275160260373	0.725352245598938	3	4	4	3	2	0	3	1
-Deaf1	1.44422489044724	1.025131982023	1.42887088408062	0.231948799198155	0.337138318324962	0.852249424298157	14	1.12923005557722	0.612579053628728	3.727933661979	0	0	1.54680939617797	0.370917200867911	0	3	1	7	0	0	2	1	0
-Mir134	-1.14682917623374	1.93261005672816	1.42668479177753	0.232306245088513	0.337171088167804	0.695658731242064	40	2.63487012968019	4.2880533754011	0	0	1.48980486323549	4.64042818853392	3.70917200867911	5.8028179647915	7	7	0	0	2	6	10	8
-Mir377	-1.61378491210757	0.717489850287155	1.42512095604139	0.232562354415479	0.337171088167804	1.06158652526604	8	0	1.22515810725746	0	0	0.744902431617745	0	0.370917200867911	2.90140898239575	0	2	0	0	1	0	1	4
-Ndufs6	1.53512539963964	0.813159285646448	1.40740426155936	0.235487778942306	0.340979131691842	0.899781590705908	10	1.12923005557722	0	2.66280975855643	0	0	0	0.370917200867911	0.725352245598938	3	0	5	0	0	0	1	1
-6720401G13Rik	2.25133431427166	0.768838918008168	1.40046926717881	0.236645015832865	0.342074043993747	2.81750531855529	9	0	0	4.26049561369029	0	0	0	0	0.725352245598938	0	0	8	0	0	0	0	1
-Airn	-1.47387977089094	2.52944495005948	1.39928361476914	0.236843553685417	0.342074043993747	1.34618529718523	66	0	0	10.6512390342257	0	2.97960972647098	13.9212845656018	4.45100641041494	8.70422694718725	0	0	20	0	4	18	12	12
-Gt(ROSA)26Sor	-1.15096936032435	1.54361967638261	1.39703782718287	0.237220165154539	0.34218484000168	0.64344326809099	26	1.12923005557722	0	2.13024780684514	1.61891659812001	2.23470729485323	6.96064228280088	0.370917200867911	2.17605673679681	3	0	4	3	3	9	1	3
-Sec23b	1.82895755193543	0.644850222597462	1.3697672560722	0.241851876350373	0.348227090579605	1.48411734198092	7	0.376410018525741	0	2.66280975855643	0	0.744902431617745	0	0	0	1	0	5	0	1	0	0	0
-E2f6	1.53973552755681	1.10259786021808	1.36879310086588	0.242019353926053	0.348227090579605	1.16390433951375	16	3.01128014820593	0	2.66280975855643	0	1.48980486323549	0	0.370917200867911	0	8	0	5	0	2	0	1	0
-Orc6	1.38084285450996	0.514031868300813	1.3655797080292	0.242572805282196	0.348583842351367	0.0702725556992107	5	0.376410018525741	0.612579053628728	0.532561951711286	0.539638866040004	0.744902431617745	0	0	0	1	1	1	1	1	0	0	0
-Clk1	1.2861003411955	2.2155754729238	1.36240392743992	0.243121294127128	0.348932574338432	0.993302407698676	54	6.02256029641185	0	9.58611513080315	3.23783319624003	4.46941458970647	0	2.96733760694329	0	16	0	18	6	6	0	8	0
-Mir339	0.42814368668433	5.34471486348628	1.34652946977175	0.245885757104158	0.352343299639	0.115900409149214	599	54.2030426677067	53.2943776656993	37.8118985715013	35.0765262926003	28.3062924014743	28.6159738292925	38.9463060911307	37.7183167711448	144	87	71	65	38	37	105	52
-Fbxo34	1.07477259541521	1.07377334724852	1.34522090175497	0.246115346023035	0.352343299639	0.309939899179282	15	1.50564007410296	1.83773716088618	2.13024780684514	0	0.744902431617745	0.773404698088987	0.370917200867911	0.725352245598938	4	3	4	0	1	1	1	1
-B230217O12Rik	1.4246114949511	0.762941248991215	1.3299183272188	0.248819747974054	0.355768587015534	0.70095764609552	9	0.376410018525741	0	0.532561951711286	2.69819433020002	0	0	0.370917200867911	0.725352245598938	1	0	1	5	0	0	1	1
-Mir101c	1.42009163016916	0.50716611553616	1.32364733686219	0.249938515353831	0.356920958721804	0.214834900602033	5	0.376410018525741	0	1.06512390342257	0.539638866040004	0	0	0.370917200867911	0	1	0	2	1	0	0	1	0
-1700113A16Rik	1.04952261884512	0.8748029109583	1.3159338910949	0.251323095910532	0.358210570839521	0.132374100720698	11	0.752820037051481	0.612579053628728	1.06512390342257	1.61891659812001	0.744902431617745	0	0.370917200867911	0.725352245598938	2	1	2	3	1	0	1	1
-Abhd11	1.36437035299394	0.70312593778772	1.31512148633035	0.251469471728708	0.358210570839521	0.514223097681327	8	0	1.22515810725746	1.06512390342257	1.07927773208001	0	0	0.741834401735823	0	0	2	2	2	0	0	2	0
-Pisd-ps3	1.11246774172608	1.06559741280053	1.30733127850408	0.252878410925609	0.359768412551271	0.398841639277644	15	1.50564007410296	0	2.66280975855643	1.07927773208001	0.744902431617745	0.773404698088987	0.741834401735823	0	4	0	5	2	1	1	2	0
-Snord82	0.518546924862024	3.81085925901395	1.29940283263746	0.254322331897629	0.361372080566867	0.152756163372285	191	17.6912708707098	11.6390020189458	21.3024780684514	9.71349958872008	12.6633413375017	10.8276657732458	7.04742681649032	12.3309881751819	47	19	40	18	17	14	19	17
-1600002D24Rik	-1.33099651490946	0.646039493001314	1.29243976651877	0.255598819161262	0.36241928722574	0.483747585291553	7	0	0	1.06512390342257	0	0	0.773404698088987	0.741834401735823	1.45070449119788	0	0	2	0	0	1	2	2
-Tug1	0.970668426400212	2.63263861953326	1.29191908284646	0.255694589146995	0.36241928722574	0.58850779920907	78	6.77538033346333	1.22515810725746	14.3791726962047	3.23783319624003	2.23470729485323	0	5.93467521388658	4.35211347359363	18	2	27	6	3	0	16	6
-Mir744	0.377651340457821	7.1472318972363	1.28525775737881	0.256923728325823	0.363709645185811	0.102366881957743	2175	165.2439981328	196.025297161193	99.5890849700105	173.763714864881	110.245559879426	102.089420147746	189.167772442635	84.8662127350757	439	320	187	322	148	132	510	117
-Rn45s	0.65102222101098	14.5532392475354	1.27910699725271	0.258065140076218	0.36487276930231	0.315704198286193	360404	47537.5740596528	12635.6681391998	46475.0838399888	10847.8204851362	22385.8078749765	25986.39785579	4549.6703858458	21904.1871125967	126292	20627	87267	20102	30052	33600	12266	30198
-Mir1945	1.35210912624303	0.509953639891973	1.26278125134319	0.261125293512193	0.36874252462551	0.144131562458991	5	0.752820037051481	0	0.532561951711286	0.539638866040004	0	0.773404698088987	0	0	2	0	1	1	0	1	0	0
-Atp10d	1.53331436368779	1.15558274925479	1.25534657129032	0.262533762624941	0.37027320538326	1.32191949957869	17	2.63487012968019	0	3.727933661979	0	1.48980486323549	0	0	0.725352245598938	7	0	7	0	2	0	0	1
-Pvt1	1.13237061461131	0.706845363550169	1.24762805726204	0.264005989484645	0.37132259609486	0.112183395552895	8	0.752820037051481	0.612579053628728	1.06512390342257	0.539638866040004	0.744902431617745	0	0	0.725352245598938	2	1	2	1	1	0	0	1
-Gm2518	1.15651903727818	0.700596843013412	1.24659671279059	0.264203483537775	0.37132259609486	0.157869476939936	8	0.752820037051481	0	1.06512390342257	1.07927773208001	0	0.773404698088987	0.370917200867911	0	2	0	2	2	0	1	1	0
-C230091D08Rik	1.56585828620223	1.16194302765321	1.24517880098089	0.26447530189213	0.37132259609486	1.41644478133515	17	1.8820500926287	0	4.79305756540158	0	0	1.54680939617797	0	0.725352245598938	5	0	9	0	0	2	0	1
-Spns1	1.29130279990573	0.750979881345235	1.24463546356304	0.264579553571535	0.37132259609486	0.507406490692187	9	1.8820500926287	0.612579053628728	0.532561951711286	0	0	0	0.370917200867911	0.725352245598938	5	1	1	0	0	0	1	1
-Wbscr25	-1.54070401657763	0.450389373474786	1.2395967363309	0.265548786718362	0.372225019220701	0.662915151912046	4	0	0	0.532561951711286	0	1.48980486323549	0.773404698088987	0	0	0	0	1	0	2	1	0	0
-Rnf126	1.352317882363	0.510697356258459	1.23574315626322	0.26629303137175	0.37281024392045	0.183948550759336	5	0.752820037051481	0.612579053628728	0.532561951711286	0	0.744902431617745	0	0	0	2	1	1	0	1	0	0	0
-Etohd2	1.55024153858454	0.577371011234276	1.22484335481533	0.268412231743709	0.37531661325928	0.885850182775071	6	0.752820037051481	0	1.59768585513386	0	0	0.773404698088987	0	0	2	0	3	0	0	1	0	0
-Gm10865	1.24385542624789	0.708647725781233	1.22065430239173	0.269232283130647	0.376002490883804	0.362664882724299	8	0	1.22515810725746	1.06512390342257	1.07927773208001	0	0	0.370917200867911	0.725352245598938	0	2	2	2	0	0	1	1
-Rbbp8	1.28319321283268	1.21201050991301	1.21613526340884	0.270120443730782	0.376781694739391	0.861651792833619	18	1.50564007410296	1.22515810725746	4.26049561369029	0	1.48980486323549	0	0	1.45070449119788	4	2	8	0	2	0	0	2
-Tubgcp4	1.33791798990343	0.977516297021678	1.20023071044651	0.273275571586703	0.380717249304552	0.874960057222824	13	0.752820037051481	0	3.727933661979	0.539638866040004	1.48980486323549	0	0.370917200867911	0	2	0	7	1	2	0	1	0
-C230037L18Rik	1.35620856225366	0.513286892568134	1.18625355142246	0.276086563999894	0.384164353077901	0.272029007915648	5	0.376410018525741	0	0.532561951711286	1.07927773208001	0	0.773404698088987	0	0	1	0	1	2	0	1	0	0
-Sh2d3c	-0.989172553511926	0.989564782427474	1.17988452537781	0.27737950514388	0.385290746846568	0.273751596021749	13	0.752820037051481	0	1.06512390342257	0.539638866040004	1.48980486323549	2.32021409426696	0.370917200867911	1.45070449119788	2	0	2	1	2	3	1	2
-Mir93	0.258061794981841	8.95936436014001	1.17894232076207	0.277571423232147	0.385290746846568	0.0530464153691209	7480	575.907328344383	575.211731357376	368.000308632499	644.328806051765	481.951873256681	371.234255082714	518.171329612472	436.662051850561	1530	939	691	1194	647	480	1397	602
-Zfp207	1.31573613172173	1.24971382078769	1.171627649335	0.279067054659271	0.386840201979411	0.997407162230148	19	1.8820500926287	0	4.79305756540158	0.539638866040004	0	1.54680939617797	0	1.45070449119788	5	0	9	1	0	2	0	2
-Ubl4	1.06854952853088	1.0735946448232	1.17017271545995	0.279365754978997	0.386840201979411	0.432683488735817	15	1.12923005557722	0	2.66280975855643	1.61891659812001	0.744902431617745	0	0.370917200867911	1.45070449119788	3	0	5	3	1	0	1	2
-Gm13375	1.39917058732533	0.5170958137341	1.16795214501518	0.279822419421483	0.387002885527166	0.416936193500448	5	0	0.612579053628728	1.06512390342257	0.539638866040004	0	0	0	0.725352245598938	0	1	2	1	0	0	0	1
-Klc2	1.37596729798951	0.514840226031161	1.16016307268757	0.281431723163354	0.388757380301921	0.367115415607697	5	0.376410018525741	1.22515810725746	0.532561951711286	0	0	0	0	0.725352245598938	1	2	1	0	0	0	0	1
-Magix	1.58289386102868	0.511362021896504	1.15039032456122	0.283467455935942	0.391095970039795	1.00966038993426	5	0	0.612579053628728	1.59768585513386	0	0	0	0.370917200867911	0	0	1	3	0	0	0	1	0
-Mir1839	0.370480164024589	6.74498720522536	1.1482134598462	0.283923447509647	0.391251997111724	0.109391022162609	1655	113.299415576248	112.101966814057	129.945116217554	121.958383725041	84.9188772044229	58.005352356674	154.301555561051	69.633815577498	301	183	244	226	114	75	416	96
-Snord8	0.806893720861943	1.69268604059307	1.14641299100765	0.284301297005762	0.391300096361369	0.290529220847026	32	3.76410018525741	2.45031621451491	3.19537171026772	1.07927773208001	0.744902431617745	2.32021409426696	1.48366880347165	1.45070449119788	10	4	6	2	1	3	4	2
-4930481A15Rik	1.5515906543429	0.917398122432339	1.12447614916941	0.28895666078315	0.397228373438042	1.46738401507094	12	2.25846011115444	0	2.13024780684514	0	1.48980486323549	0	0	0	6	0	4	0	2	0	0	0
-Dleu2	0.317688954127526	8.19301158324783	1.10602978293134	0.292946616794128	0.402228748209507	0.0855423121930951	4399	326.723896080343	391.438015268757	153.910404044562	421.457954377243	248.797412160327	225.834171841984	319.73062714814	242.267650030045	868	639	289	781	334	292	862	334
-Mir434	-0.54919588286671	5.38683878237064	1.09770962227219	0.294769296453562	0.40424491256432	0.249691576615719	623	60.97842300117	39.8176384858673	6.92330537224672	23.7441101057602	49.1635604867712	43.3106630929833	59.7176693397337	40.6197257535405	162	65	13	44	66	56	161	56
-4930474G06Rik	-1.42872669597032	0.444547317099226	1.08660880847268	0.29722381052778	0.406328755898014	0.663099903648888	4	0	0	0.532561951711286	0	0.744902431617745	0.773404698088987	0.370917200867911	0	0	0	1	0	1	1	1	0
-A430093F15Rik	-1.42872669597032	0.444547317099226	1.08660880847268	0.29722381052778	0.406328755898014	0.663099903648888	4	0	0	0.532561951711286	0	0.744902431617745	0.773404698088987	0.370917200867911	0	0	0	1	0	1	1	1	0
-2900076A07Rik	0.357704988524868	6.75351475086346	1.08600912377275	0.297357152651045	0.406328755898014	0.107790840284727	1663	113.299415576248	112.101966814057	131.010240120976	121.958383725041	86.4086820676584	59.552161752852	154.672472761919	70.359167823097	301	183	246	226	116	77	417	97
-March2	1.1490450228439	1.81024670587524	1.08392796465331	0.297820502428094	0.406430184516712	0.923172571807024	36	5.26974025936037	0	6.39074342053543	1.07927773208001	2.97960972647098	1.54680939617797	0	1.45070449119788	14	0	12	2	4	2	0	2
-Mir3058	-1.2044465540242	0.776024090779448	1.08247836361925	0.298143790044249	0.406430184516712	0.624160194032919	9	0	0	1.06512390342257	0.539638866040004	1.48980486323549	2.32021409426696	0.370917200867911	0	0	0	2	1	2	3	1	0
-H2-T10	1.49091432235158	0.50705923050694	1.07820063115921	0.299100436056709	0.406871218665541	0.887359264881885	5	0.376410018525741	0	1.59768585513386	0	0	0	0.370917200867911	0	1	0	3	0	0	0	1	0
-Snord111	0.606752197652989	2.71306413132783	1.07784340804694	0.299180501718132	0.406871218665541	0.224746103077504	82	8.65743042609204	8.57610675080219	5.32561951711286	3.23783319624003	4.46941458970647	3.09361879235595	4.82192361128285	4.35211347359363	23	14	10	6	6	4	13	6
-Minos1	0.999689645568584	1.34246645297262	1.07429307988648	0.299977750227641	0.407469777392546	0.533576137747072	22	4.14051020378315	0.612579053628728	0.532561951711286	1.61891659812001	0.744902431617745	1.54680939617797	1.11275160260373	0	11	1	1	3	1	2	3	0
-Gm10336	-1.41305683603525	0.444085980903392	1.06720095262707	0.301578541238564	0.408671158614253	0.663114492823995	4	0	0	0	0.539638866040004	0	0	0.370917200867911	1.45070449119788	0	0	0	1	0	0	1	2
-Gm16897	-1.41305683603525	0.444085980903392	1.06720095262707	0.301578541238564	0.408671158614253	0.663114492823995	4	0	0	0	0.539638866040004	0	0	0.370917200867911	1.45070449119788	0	0	0	1	0	0	1	2
-Snord83b	0.412016510679215	3.99035331424224	1.05314046138814	0.304784917500656	0.412526205063166	0.115963050278327	221	18.0676808892356	13.476739179832	18.1071063581837	17.2684437132801	16.3878534955904	9.28085637706784	12.9821020303769	11.605635929583	48	22	34	32	22	12	35	16
-Fam19a2	-1.39439412627523	0.445236305727518	1.04277449700462	0.307177074139207	0.415271376294828	0.663078115251079	4	0	0.612579053628728	0	0	0.744902431617745	0	0.370917200867911	0.725352245598938	0	1	0	0	1	0	1	1
-Gm6793	1.43759807516069	0.570980107794987	1.02892445660156	0.310411415796383	0.419147249022098	0.985765099419335	6	1.50564007410296	0	0.532561951711286	0	0	0.773404698088987	0	0	4	0	1	0	0	1	0	0
-Mir677	-0.556581193997838	2.91938107006516	1.0216654718832	0.312124280053064	0.420961942719321	0.207540332077216	94	5.26974025936037	3.67547432177237	5.85818146882415	6.47566639248005	11.9184389058839	9.28085637706784	6.30559241475449	4.35211347359363	14	6	11	12	16	12	17	6
-Mir15a	0.323472503909827	8.01067798948637	1.01525465436931	0.313647269081676	0.422516569093497	0.0966057811485782	3883	289.83571426482	347.944902461118	124.08693474873	379.366122826123	219.001314895617	197.991602710781	287.089913471763	206.725389995697	770	568	233	703	294	256	774	285
-Rmi1	1.19649467559254	0.703415054910478	1.01273531337804	0.314248433228481	0.422827196124643	0.5365572749587	8	0.376410018525741	0	2.13024780684514	0.539638866040004	0.744902431617745	0	0.370917200867911	0	1	0	4	1	1	0	1	0
-Myeov2	1.3752791899028	0.500631880884289	1.00847894668689	0.315267512241198	0.423698741421916	0.68508973865721	5	1.12923005557722	0	0.532561951711286	0	0	0	0.370917200867911	0	3	0	1	0	0	0	1	0
-Snhg5	-0.891252404860635	0.988818036196163	1.00092989845109	0.317085604229749	0.425640793442522	0.242108615776824	13	0.376410018525741	1.22515810725746	0	1.07927773208001	2.23470729485323	0.773404698088987	0.741834401735823	1.45070449119788	1	2	0	2	3	1	2	2
-Alg9	1.38266937531922	0.822272867813765	0.991092828673628	0.319475424234761	0.428344840248957	1.20246527903028	10	0.752820037051481	0	3.19537171026772	0	0.744902431617745	0.773404698088987	0	0	2	0	6	0	1	1	0	0
-Mir296	-1.03122376978725	0.868255875953981	0.969681917990509	0.324759520438443	0.434918559648196	0.477911424633548	11	1.12923005557722	0	0.532561951711286	0	0.744902431617745	0	1.11275160260373	2.17605673679681	3	0	1	0	1	0	3	3
-Cnot2	1.16147988975839	1.30506961499225	0.964321975522214	0.326100356033999	0.436202234741844	0.976345068131713	21	4.14051020378315	0	2.66280975855643	0	0	1.54680939617797	0.741834401735823	0.725352245598938	11	0	5	0	0	2	2	1
-Gm10649	-1.17056180193158	0.590943716672117	0.950295151786785	0.329644180348444	0.440426240957348	0.455805593207835	6	0	0	0.532561951711286	0.539638866040004	1.48980486323549	0.773404698088987	0	0.725352245598938	0	0	1	1	2	1	0	1
-4933433G15Rik	-1.31542050079849	0.438830702629464	0.944809554977709	0.331044008881153	0.440822944076184	0.663280688352345	4	0	0	0	0.539638866040004	0	0.773404698088987	0.741834401735823	0	0	0	0	1	0	1	2	0
-Mir487b	-1.31542050079849	0.438830702629464	0.944809554977709	0.331044008881153	0.440822944076184	0.663280688352345	4	0	0	0	0.539638866040004	0	0.773404698088987	0.741834401735823	0	0	0	0	1	0	1	2	0
-Ufd1l	1.83013215132634	0.648264703504357	0.944466213970336	0.331131886353484	0.440822944076184	2.8244372867478	7	0	0	3.19537171026772	0	0	0.773404698088987	0	0	0	0	6	0	0	1	0	0
-2810055G20Rik	-0.774119158390019	1.25290177573675	0.9430819910342	0.331486490812766	0.440822944076184	0.235971306397399	19	1.50564007410296	0	1.06512390342257	1.07927773208001	2.23470729485323	2.32021409426696	1.11275160260373	1.45070449119788	4	0	2	2	3	3	3	2
-Snord49a	0.347708396282739	6.19517637060946	0.940500720776813	0.332149102351942	0.441189901959914	0.11555421344434	1114	87.3271242979718	92.4994370979379	63.9074342053543	78.2476355758006	62.5718042558906	39.4436396025383	94.9548034221853	54.4014184199203	232	151	120	145	84	51	256	75
-Mir26a-2	0.571532904896869	3.30364549427615	0.935051290028968	0.333553781231292	0.442540539982446	0.271793027590196	131	6.39897031493759	17.7647925552331	5.85818146882415	11.8720550528801	7.44902431617745	2.32021409426696	11.4984332269053	5.8028179647915	17	29	11	22	10	3	31	8
-Mrpl48	0.951209129028088	0.877695610887092	0.909879188951829	0.340146475473504	0.450651070518895	0.309435986552712	11	1.12923005557722	0.612579053628728	0.532561951711286	1.61891659812001	1.48980486323549	0.773404698088987	0	0	3	1	1	3	2	1	0	0
-Snord64	-0.420539246374586	3.85466381978465	0.908514520780082	0.340508867501239	0.450651070518895	0.14580120158986	197	9.03384044461778	7.96352769717346	10.1186770825144	18.8873603114001	16.3878534955904	14.6946892636907	17.8040256416597	12.3309881751819	24	13	19	35	22	19	48	17
-Mir505	0.791118576264698	1.12459084148596	0.907225029268214	0.340851773757938	0.450651070518895	0.193148986386638	16	1.12923005557722	1.22515810725746	1.06512390342257	2.15855546416002	1.48980486323549	0.773404698088987	0.370917200867911	0.725352245598938	3	2	2	4	2	1	1	1
-Snora41	0.4457607085968	4.73756446685567	0.903210356341466	0.341922352695175	0.45154329215879	0.189120057480695	394	33.8769016673167	23.2780040378917	13.3140487927822	45.8693036134004	23.8368778117678	15.4680939617797	31.5279620737725	13.7816926663798	90	38	25	85	32	20	85	19
-Snord35b	0.938553767729952	1.07463232563284	0.893886598728487	0.344426245265019	0.454324099245534	0.451610775464664	15	1.8820500926287	0.612579053628728	1.06512390342257	1.61891659812001	2.23470729485323	0.773404698088987	0	0	5	1	2	3	3	1	0	0
-E030003E18Rik	1.12534457527493	0.696844091788613	0.871620817105213	0.350506988468022	0.461811170718259	0.594196025379944	8	1.12923005557722	0	1.59768585513386	0	0	0	0.370917200867911	0.725352245598938	3	0	3	0	0	0	1	1
-2310040G24Rik	1.22956203810021	0.688428201330028	0.849643885344393	0.356653100388518	0.469366998319838	0.959032625979528	8	1.50564007410296	0	0	1.07927773208001	0	0	0.741834401735823	0	4	0	0	2	0	0	2	0
-Gm16973	1.22567680162253	0.688218992824782	0.845862311695874	0.357725511183329	0.470235954216795	0.956184054973524	8	1.50564007410296	0	1.06512390342257	0	0	0	0.741834401735823	0	4	0	2	0	0	0	2	0
-Gm11696	1.37713756744948	0.517710856875195	0.840001428570431	0.35939636224903	0.471888664356897	1.18654599183539	5	0	0.612579053628728	0	1.61891659812001	0	0.773404698088987	0	0	0	1	0	3	0	1	0	0
-Mir500	-0.654322949379912	2.08516539683144	0.825337101869348	0.363624329468657	0.476891218303147	0.33807354510354	47	3.76410018525741	4.2880533754011	0.532561951711286	1.07927773208001	3.72451215808872	3.09361879235595	4.82192361128285	3.62676122799469	10	7	1	2	5	4	13	5
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-Gm13483	-0.405259819671348	0.441450511506885	0.0788340661792768	0.778883709727697	0.851058789268948	0.66319783685053	4	0.752820037051481	0	0	0	0.744902431617745	0.773404698088987	0	0	2	0	0	0	1	1	0	0
-Cdh23	0.259325213039628	1.01902545028967	0.0778130192654904	0.780283310880749	0.851058789268948	0.323423403817483	14	0.752820037051481	1.22515810725746	1.59768585513386	0.539638866040004	0	0	1.48366880347165	1.45070449119788	2	2	3	1	0	0	4	2
-4921531C22Rik	0.36492190894025	0.515191961700188	0.0777501925158877	0.780369753148749	0.851058789268948	0.563424790023552	5	0	1.22515810725746	0	0.539638866040004	0	0.773404698088987	0.370917200867911	0	0	2	0	1	0	1	1	0
-4930526L06Rik	-0.400926323794482	0.441282103013107	0.0773326008647368	0.78094526938176	0.851058789268948	0.663203162666082	4	0.752820037051481	0	0	0	0	0.773404698088987	0	0.725352245598938	2	0	0	0	0	1	0	1
-4930565N06Rik	-0.275692016771913	0.704972067181646	0.0745521957341646	0.784820561643055	0.853759421790747	0.187746764272044	8	0.752820037051481	0	1.06512390342257	0	0.744902431617745	0.773404698088987	0.370917200867911	0.725352245598938	2	0	2	0	1	1	1	1
-Gm16039	0.203635382066238	1.53814985640646	0.0744816255847662	0.784919924152931	0.853759421790747	0.266864141711601	27	3.01128014820593	1.22515810725746	1.06512390342257	2.15855546416002	1.48980486323549	2.32021409426696	1.48366880347165	1.45070449119788	8	2	2	4	2	3	4	2
-1600020E01Rik	-0.390597471075851	0.440882265837424	0.0738197774696623	0.785854275651585	0.853961646208055	0.663215807320604	4	0.752820037051481	0	0	0	0	0	0	1.45070449119788	2	0	0	0	0	0	0	2
-Fance	0.50084333160149	0.585954539136612	0.0720524692697513	0.788371497616278	0.855270403178805	3.12433936308979	6	0	0	2.13024780684514	0	1.48980486323549	0	0	0	0	0	4	0	2	0	0	0
-E230016M11Rik	0.342721174693447	0.513769470217108	0.071798200298467	0.78873637275728	0.855270403178805	0.488493855150565	5	0	0.612579053628728	1.06512390342257	0	0.744902431617745	0	0.370917200867911	0	0	1	2	0	1	0	1	0
-1700086O06Rik	0.236269656222079	1.48883272976725	0.071401243017057	0.789307392241264	0.855270403178805	0.475993254072891	26	3.01128014820593	1.22515810725746	0.532561951711286	2.15855546416002	0.744902431617745	2.32021409426696	2.59642040607538	0	8	2	1	4	1	3	7	0
-4930473A02Rik	0.352471611630964	0.500477705690642	0.0701446174715246	0.791126333619388	0.856428032883987	0.646696111280693	5	0.752820037051481	0	0.532561951711286	0	0	0	0.741834401735823	0	2	0	1	0	0	0	2	0
-A230020J21Rik	-0.267026788333725	0.705749087999938	0.0694037193790127	0.792206949992774	0.856784957290763	0.203583555202171	8	0.752820037051481	0.612579053628728	0	0.539638866040004	0.744902431617745	0	0.370917200867911	1.45070449119788	2	1	0	1	1	0	1	2
-4930583K01Rik	-0.311376486734353	0.585998814634588	0.0669415918612577	0.795843005751654	0.859902338600983	0.427642087614576	6	0.376410018525741	0.612579053628728	0	0.539638866040004	0.744902431617745	0	0	1.45070449119788	1	1	0	1	1	0	0	2
-Snord70	0.145331626973667	2.86064497684293	0.0657897221647867	0.797568584866601	0.860951518763284	0.22205290795422	92	8.65743042609204	6.12579053628728	3.19537171026772	7.55494412456006	4.46941458970647	8.50745167897886	5.93467521388658	4.35211347359363	23	10	6	14	6	11	16	6
-Arhgap1	0.339569541187162	1.2096566695747	0.0649812879626062	0.798789310008591	0.86145425587883	1.44007572113653	18	2.25846011115444	0	3.19537171026772	0	2.23470729485323	2.32021409426696	0	0	6	0	6	0	3	3	0	0
-AI450353	0.34055845147888	0.910101618432891	0.0632466127557674	0.80143622610689	0.863492666655299	1.43735572039674	12	3.01128014820593	0	0	0	0.744902431617745	0	0.370917200867911	1.45070449119788	8	0	0	0	1	0	1	2
-Abhd10	-0.276151496509407	0.585317127970325	0.0624086234287011	0.80272873318597	0.863759660272467	0.171774391618741	6	0.376410018525741	0	0.532561951711286	0.539638866040004	0.744902431617745	0.773404698088987	0	0.725352245598938	1	0	1	1	1	1	0	1
-Mir5114	-0.308027420198141	0.576749028964489	0.0613324222389799	0.804402253191527	0.863759660272467	0.546573167112303	6	0.752820037051481	0	0	0.539638866040004	0	1.54680939617797	0.370917200867911	0	2	0	0	1	0	2	1	0
-Svip	-0.350973217175904	0.444935973798038	0.0605317045420897	0.805657524963423	0.863759660272467	0.663087612872524	4	0.376410018525741	0	0.532561951711286	0	0	1.54680939617797	0	0	1	0	1	0	0	2	0	0
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-Mir1306	-0.1851941109557	1.27726022626805	0.0596401679260163	0.807065576173644	0.863759660272467	0.210448917094876	20	1.50564007410296	1.22515810725746	1.06512390342257	1.07927773208001	0.744902431617745	0.773404698088987	2.22550320520747	1.45070449119788	4	2	2	2	1	1	6	2
-Mir1946b	0.227524210048939	1.08130128376378	0.0593307772060241	0.807556817807109	0.863759660272467	0.41086424728352	15	0.752820037051481	0	2.13024780684514	1.61891659812001	0.744902431617745	0.773404698088987	0.370917200867911	2.17605673679681	2	0	4	3	1	1	1	3
-Gm19522	-0.282927454068429	0.707964870962573	0.0590387683103746	0.808021707255509	0.863759660272467	0.579476887179664	8	0.376410018525741	0	1.59768585513386	0	0	0.773404698088987	0.370917200867911	1.45070449119788	1	0	3	0	0	1	1	2
-B230319C09Rik	-0.344937059890506	0.444704025045226	0.0587065035008631	0.808552169027653	0.863759660272467	0.66309494795869	4	0.376410018525741	0	0.532561951711286	0	0.744902431617745	0.773404698088987	0	0	1	0	1	0	1	1	0	0
-2310010J17Rik	-0.343109552136964	0.802996102846669	0.0584115657810287	0.809024371063529	0.863759660272467	1.47638377658733	10	1.8820500926287	0	0	0	1.48980486323549	0	1.11275160260373	0	5	0	0	0	2	0	3	0
-Gm10433	-0.342785645739424	0.444811958880092	0.0580499984927432	0.809604973396614	0.863759660272467	0.663091534687766	4	0.376410018525741	0	0	0.539638866040004	0.744902431617745	0.773404698088987	0	0	1	0	0	1	1	1	0	0
-2610035D17Rik	-0.34060377449556	0.444535312857616	0.0574097286271007	0.810637826877285	0.863759660272467	0.663100283267815	4	0.376410018525741	0	0.532561951711286	0	0	0.773404698088987	0	0.725352245598938	1	0	1	0	0	1	0	1
-1700007J10Rik	0.315763104090594	0.642271288008478	0.0573291334197377	0.810768270071702	0.863759660272467	0.825778513948771	7	0	0.612579053628728	1.59768585513386	0	0	0	0.741834401735823	0.725352245598938	0	1	3	0	0	0	2	1
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-C730002L08Rik	0.281569792976699	0.50929338696675	0.0545302058651105	0.815359942761565	0.867032334287927	0.336468455814845	5	0.376410018525741	0	1.06512390342257	0	0	0	0.370917200867911	0.725352245598938	1	0	2	0	0	0	1	1
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-Mir423	-0.0744500249085018	8.84921671367008	0.0477299944999316	0.827061408334372	0.877839132008854	0.11037853557516	6997	452.821252286466	622.380318486788	186.929245050661	530.465005317324	495.3601170258	328.696996687819	675.811139981334	385.887394658635	1203	1016	351	983	665	425	1822	532
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-Gm7367	0.248315611787725	0.506240872372134	0.0451945920786558	0.831646617931449	0.88071299185006	0.282626853737845	5	0.752820037051481	0	0.532561951711286	0	0.744902431617745	0	0.370917200867911	0	2	0	1	0	1	0	1	0
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-Lmf1	-0.22548796047855	0.97883425965457	0.0445376183881478	0.832856545316577	0.88071299185006	0.558630351034554	13	1.50564007410296	0	1.59768585513386	0	0.744902431617745	2.32021409426696	0.370917200867911	0.725352245598938	4	0	3	0	1	3	1	1
-Rhno1	-0.289809107838461	0.448195063662935	0.0427642739891088	0.836169768630754	0.883397875933047	0.662984547299674	4	0	0	1.06512390342257	0	0	1.54680939617797	0	0	0	0	2	0	0	2	0	0
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-Cd22	-0.269112364005035	0.447392391552775	0.0376139174811776	0.846220452711214	0.88907692131077	0.663009931311267	4	0	0	1.06512390342257	0	0	0	0	1.45070449119788	0	0	2	0	0	0	0	2
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-Rbmx	0.0986438999750026	4.04533361891745	0.0351385202262877	0.851305694713209	0.892775549326996	0.231893714397283	240	18.0676808892356	20.215108769748	17.5745444064724	6.47566639248005	12.6633413375017	6.96064228280088	27.8187900650933	9.42957919278619	48	33	33	12	17	9	75	13
-2610002J02Rik	-0.186800122590241	0.574544504406253	0.0317659253685125	0.858542366895874	0.898715160320257	0.156379445413999	6	0.376410018525741	0.612579053628728	0.532561951711286	0	0	0	0.741834401735823	0.725352245598938	1	1	1	0	0	0	2	1
-4930527F14Rik	-0.244281035069941	0.448591927059054	0.0317648575898586	0.858544719324347	0.898715160320257	0.662971996634629	4	0	0.612579053628728	0	0.539638866040004	0	0	0	1.45070449119788	0	1	0	1	0	0	0	2
-Mir376b	-0.158192220319799	1.94229985404655	0.0291620903328313	0.864405315667954	0.904020591363094	0.66104946054871	42	6.02256029641185	3.06289526814364	0.532561951711286	0	1.48980486323549	3.09361879235595	4.08008920954702	2.17605673679681	16	5	1	0	2	4	11	3
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-Mir1966	-0.168385030472115	0.694856549428838	0.0281514995472145	0.866753142466161	0.904817324385992	0.282676636878772	8	0.752820037051481	0.612579053628728	0.532561951711286	0	0	0.773404698088987	1.11275160260373	0	2	1	1	0	0	1	3	0
-Mir541	-0.077168646472825	6.66411334271104	0.0276499777784416	0.867934381808835	0.905222239162597	0.201614530468415	1553	181.806038947933	115.164862082201	25.5629736821417	66.3755805229205	90.1331942257471	95.9021825630344	118.693504277732	105.901427857445	483	188	48	123	121	124	320	146
-2010320M18Rik	-0.153440953029695	0.817265649192632	0.0272545561526618	0.868873506070553	0.90537412824338	0.260143808082405	10	0.376410018525741	1.22515810725746	0.532561951711286	0.539638866040004	0	0	1.11275160260373	1.45070449119788	1	2	1	1	0	0	3	2
-Mir598	0.117106193594072	2.01449875553177	0.026591961868164	0.870462989465158	0.905727359455395	0.318163899001966	44	3.01128014820593	4.90063242902982	1.06512390342257	3.23783319624003	1.48980486323549	1.54680939617797	4.08008920954702	3.62676122799469	8	8	2	6	2	2	11	5
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-Mir147	-0.214870858659421	0.438986983809201	0.0252765012139977	0.873680020327864	0.907069065690713	0.663275745839807	4	0.376410018525741	0	0	0.539638866040004	0	0.773404698088987	0.370917200867911	0	1	0	0	1	0	1	1	0
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-Mir18	-0.0990461811170021	2.43255748654297	0.0244202461482868	0.875820370671476	0.907639457707679	0.262434880797305	62	2.63487012968019	5.51321148265855	2.13024780684514	7.01530525852006	5.21431702132421	5.41383288662291	2.96733760694329	5.07746571919256	7	9	4	13	7	7	8	7
-Gm10785	0.246751251689755	0.623026703715629	0.0216449504941716	0.883035543976129	0.913456047304436	2.19651377696425	7	1.50564007410296	0	0	0	0	0	1.11275160260373	0	4	0	0	0	0	0	3	0
-Plscr3	-0.194781611758836	0.439965845826999	0.0214241883614958	0.88362927784719	0.913456047304436	0.663244788949233	4	0.376410018525741	0.612579053628728	0	0	0	0.773404698088987	0.370917200867911	0	1	1	0	0	0	1	1	0
-Ftx	0.0442562859903849	6.90323954909954	0.0213480503202534	0.883834773202539	0.913456047304436	0.0833237481353848	1746	143.788627076833	106.588755331399	88.4052839840735	142.464660634561	117.694584195604	100.542610751568	97.1803066273928	152.323971575777	382	174	166	264	158	130	262	210
-1810034E14Rik	-0.0921399384668532	2.43383344256362	0.0208468626811538	0.885196913624535	0.913699659162986	0.275109743702893	64	4.14051020378315	6.12579053628728	2.13024780684514	4.31711092832003	6.7041218845597	1.54680939617797	5.56375801301867	3.62676122799469	11	10	4	8	9	2	15	5
-Snord61	0.0765324626138409	4.00249776431419	0.0206734655688221	0.885672062256146	0.913699659162986	0.236868929009887	233	17.3148608521841	18.9899506624906	17.0419824547612	6.47566639248005	11.9184389058839	6.18723758471189	27.8187900650933	9.42957919278619	46	31	32	12	16	8	75	13
-1110019D14Rik	0.167902116965848	0.515697023285334	0.0202799345502163	0.886758031871484	0.913993599246037	0.549541191684381	5	0.376410018525741	0	0	1.07927773208001	0.744902431617745	0.773404698088987	0	0	1	0	0	2	1	1	0	0
-Mirlet7g	0.0421573852946991	11.2520713569692	0.0161689789965749	0.898815900469386	0.925585688118744	0.105394399515463	38152	2846.03615007313	2901.17439798566	1421.94041106913	2723.5573569039	2055.93071126498	1812.0872076225	3890.17960270265	1847.47216954049	7561	4736	2670	5047	2760	2343	10488	2547
-Zmynd8	-0.0949628221618098	1.65780389373413	0.0137976811983114	0.906492741701422	0.932316200794775	0.385874123780723	30	1.12923005557722	1.83773716088618	4.26049561369029	1.07927773208001	3.72451215808872	3.09361879235595	1.48366880347165	0.725352245598938	3	3	8	2	5	4	4	1
-2810001G20Rik	-0.147420769233846	0.429608186028715	0.0136518460370976	0.906985962210517	0.932316200794775	0.663572390092808	4	0.752820037051481	0	0	0	0	0	0.741834401735823	0	2	0	0	0	0	0	2	0
-Mir10a	-0.0474697256380783	14.9476035526803	0.0130438853684609	0.909071459340354	0.933618843480958	0.165973498871164	435679	26662.2508422338	36481.5329598053	22924.1292114123	38247.9839083174	26200.4532272909	53305.3720063872	15001.3752719018	33968.2456613983	70833	59554	43045	70877	35173	68923	40444	46830
-4930547E14Rik	-0.14153238969448	0.441943990602939	0.0125841055606246	0.91068155907622	0.934431347937021	0.663182230938598	4	0	0	0	1.07927773208001	0	0	0.370917200867911	0.725352245598938	0	0	0	2	0	0	1	1
-Pfkfb2	0.105273545930274	1.33195915147488	0.0121131136969357	0.912362114667365	0.935314620696733	0.577808434849238	21	1.12923005557722	0	4.26049561369029	0.539638866040004	0.744902431617745	2.32021409426696	1.11275160260373	1.45070449119788	3	0	8	1	1	3	3	2
-Gm15441	0.0780434196843491	2.02230388105404	0.0101692823290582	0.919675203206381	0.941269117247064	0.417333073300976	43	2.25846011115444	0.612579053628728	5.85818146882415	3.77747206228003	4.46941458970647	2.32021409426696	1.11275160260373	4.35211347359363	6	1	11	7	6	3	3	6
-2310001K24Rik	-0.123279260083522	0.442816530704177	0.0101324291999836	0.919820390648971	0.941269117247064	0.663154637691832	4	0	0.612579053628728	0.532561951711286	0	0	0	0.370917200867911	0.725352245598938	0	1	1	0	0	0	1	1
-A930015D03Rik	0.085915192692888	1.36572130390349	0.0094268686214436	0.9226532842026	0.943322040569145	0.492017118766785	22	2.63487012968019	0.612579053628728	1.59768585513386	1.07927773208001	3.72451215808872	1.54680939617797	0.741834401735823	0	7	1	3	2	5	2	2	0
-Zc3h7a	-0.0668358500994503	5.69031492491042	0.00701387165125844	0.93325610843037	0.953308164475427	0.601890410917772	754	126.473766224649	10.4138439116884	52.7236332194173	7.55494412456006	110.245559879426	46.4042818853392	7.41834401735823	43.5211347359363	336	17	99	14	148	60	20	60
-Gm15713	0.0969082615946669	0.644365940186003	0.00606852125884316	0.937907031361341	0.957202077623694	0.875705851318187	7	0.376410018525741	0	1.59768585513386	0	0	1.54680939617797	0.370917200867911	0	1	0	3	0	0	2	1	0
-Mir101a	0.018746362146971	10.33617221496	0.00533099107497037	0.941795266334768	0.960311348425353	0.0629120871864917	19692	1149.17978655909	1264.36316668969	1605.67428440953	1180.72983889553	1087.55755016191	1068.07188806089	1844.94215711699	1129.37344639755	3053	2064	3015	2188	1460	1381	4974	1557
-E130102H24Rik	0.018463798356716	10.3369640511302	0.00517084902477905	0.942674633393959	0.960349782770096	0.0629202272317902	19702	1149.93260659614	1264.36316668969	1607.27197026466	1180.72983889553	1089.79225745676	1068.07188806089	1845.31307431786	1130.09879864315	3055	2064	3018	2188	1463	1381	4975	1558
-Mir17	0.0263848006913556	5.19330849849068	0.00482973041650681	0.944594608042067	0.961447321834075	0.122797096650431	534	36.1353617784711	38.5924803786099	27.1606595372756	41.0125538190403	40.969633738976	27.8425691312035	45.2518985058852	25.3873285959628	96	63	51	76	55	36	122	35
-Mir1940	0.0461015892261866	0.765417696099668	0.00275503654868459	0.958139504549962	0.974364683325763	0.0575915210817209	9	0.752820037051481	0.612579053628728	0.532561951711286	0.539638866040004	0.744902431617745	0.773404698088987	0.370917200867911	0.725352245598938	2	1	1	1	1	1	1	1
-Srsf9	0.0560106917056344	1.03618949071648	0.00198539953037802	0.964459762154467	0.979600223943461	1.24067995254517	14	0.376410018525741	0	3.727933661979	0	1.48980486323549	0	0.370917200867911	2.17605673679681	1	0	7	0	2	0	1	3
-1500017E21Rik	0.0442484285848218	1.30258841717713	0.00181010024428474	0.9660640218644	0.979600223943461	0.889719238393267	20	1.50564007410296	0	3.727933661979	0.539638866040004	0.744902431617745	2.32021409426696	0	2.90140898239575	4	0	7	1	1	3	0	4
-Dio3os	-0.0496676415204205	0.773498972596457	0.00166750508360192	0.967427359942802	0.979600223943461	0.367416862910443	9	0.376410018525741	0	1.06512390342257	1.07927773208001	0.744902431617745	1.54680939617797	0	0.725352245598938	1	0	2	2	1	2	0	1
-6330549D23Rik	0.0365504895755011	0.766481265149971	0.001655051458886	0.967549153599363	0.979600223943461	0.14479535661279	9	0.752820037051481	1.22515810725746	0	0.539638866040004	0.744902431617745	0.773404698088987	0.370917200867911	0.725352245598938	2	2	0	1	1	1	1	1
-Gm16291	-0.0497984136905252	1.04049827004916	0.0016518446929279	0.967580589293848	0.979600223943461	0.760533853439002	14	0.752820037051481	0.612579053628728	2.66280975855643	0	2.23470729485323	1.54680939617797	0	0.725352245598938	2	1	5	0	3	2	0	1
-Gm4890	-0.0259416163379982	0.436081268353407	0.00151936527292662	0.968907102497693	0.98007358506194	0.663367644323529	4	0	0	1.06512390342257	0	0	0	0.741834401735823	0	0	0	2	0	0	0	2	0
-5430402O13Rik	-0.0215659699048923	0.436296133284018	0.00131072481225036	0.97111974944258	0.980573127534499	0.663360848615298	4	0	0	0	1.07927773208001	0	0	0.741834401735823	0	0	0	0	2	0	0	2	0
-Gm6297	-0.0215659699048923	0.436296133284018	0.00131072481225036	0.97111974944258	0.980573127534499	0.663360848615298	4	0	0	0	1.07927773208001	0	0	0.741834401735823	0	0	0	0	2	0	0	2	0
-G730013B05Rik	-0.0385365765720758	1.01651726367811	0.000926357528096666	0.975719236926612	0.983633409858321	0.703663961483588	14	2.25846011115444	0	1.06512390342257	0	1.48980486323549	1.54680939617797	0.741834401735823	0	6	0	2	0	2	2	2	0
-Fut8	-0.0301535765572007	0.983272857012977	0.000914530318683049	0.975874688834022	0.983633409858321	0.461988777734701	13	0.376410018525741	0.612579053628728	2.66280975855643	0	0.744902431617745	1.54680939617797	0.741834401735823	0.725352245598938	1	1	5	0	1	2	2	1
-Mir451	0.00783986907363816	10.6424503554937	0.000668429571945239	0.979373786503057	0.986289047131498	0.0880041429724181	23834	1259.46792198713	1282.12795924493	1240.8693474873	2624.26380555254	1712.5306902892	1143.86554847361	1957.70098618084	1556.60591905532	3346	2093	2330	4863	2299	1479	5278	2146
-Mir3103	-0.00110923167299781	0.437273490728585	0.000542752971082194	0.98141331743335	0.987471424331087	0.663329937374331	4	0	0.612579053628728	0	0.539638866040004	0	0	0.741834401735823	0	0	1	0	1	0	0	2	0
-Mir877	0.0169238059397644	2.07117778204749	0.000493226399528979	0.982281476919532	0.987474154330561	0.411290532452574	45	2.25846011115444	4.2880533754011	0.532561951711286	5.93602752644005	2.23470729485323	3.09361879235595	1.85458600433956	5.8028179647915	6	7	1	11	3	4	5	8
-Mirlet7a-2	0.00692268187138235	3.52904314853656	0.00022929237906455	0.987918571855857	0.99163860902885	0.145210168896343	158	13.1743506484009	10.4138439116884	7.98842927566929	9.71349958872008	8.93882917941294	9.28085637706784	13.7239364321127	8.70422694718725	35	17	15	18	12	12	37	12
-Adarb1	-0.0208372088988089	1.01574105327976	0.00022013643217722	0.988162224772833	0.99163860902885	0.682420434692619	14	2.25846011115444	0	1.06512390342257	0	1.48980486323549	0	0.741834401735823	1.45070449119788	6	0	2	0	2	0	2	2
-Zfp821	0.0194908209614398	0.438251386312134	0.000105717134499805	0.991796388203091	0.994410965676386	0.663299009834258	4	0	1.22515810725746	0	0	0	0	0.741834401735823	0	0	2	0	0	0	0	2	0
-Snord7	-0.00363412912959558	0.808396104681926	2.65748040924052e-05	0.995886863013664	0.997635566899553	1.23423123101011	10	2.25846011115444	0	0	0	0.744902431617745	0	0.370917200867911	1.45070449119788	6	0	0	0	1	0	1	2
-D330022K07Rik	8.83246306189435e-05	2.3059219632559	9.35431281767762e-07	0.999228304552315	0.999852121805908	0.587915295555411	56	4.89333024083463	0.612579053628728	9.05355317909186	1.07927773208001	4.46941458970647	7.73404698088987	1.11275160260373	2.90140898239575	13	1	17	2	6	10	3	4
-AA465934	-0.00551213095838972	1.05434721413031	3.43501120880774e-08	0.999852121805908	0.999852121805908	1.5006402731101	15	3.38769016673167	0	0	0	0.744902431617745	0	0.741834401735823	2.17605673679681	9	0	0	0	1	0	2	3
--- a/test-data/gentestdata.sh	Fri Apr 10 22:46:53 2015 -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/test-data/test_bams2mx.xls	Fri Apr 10 22:46:53 2015 -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
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-0610040F04Rik	2	1	0	1	2	5	2	0
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-Mir742	0	0	0	0	0	0	0	0
-Mir743	1	0	0	0	0	0	0	0
-Mir743b	3	0	0	0	1	1	2	0
-Mir744	439	148	132	510	320	187	322	117
-Mir758	0	1	0	0	2	0	0	0
-Mir759	0	0	0	0	0	0	0	0
-Mir760	1	0	1	0	0	0	0	0
-Mir761	0	0	0	0	0	0	0	0
-Mir762	0	0	0	0	0	0	0	0
-Mir764	0	0	0	0	0	0	0	0
-Mir767	0	0	0	0	0	0	0	0
-Mir770	0	0	0	0	0	0	0	0
-Mir7b	0	0	0	1	0	0	0	0
-Mir802	552	0	0	0	401	209	352	0
-Mir804	0	0	0	0	0	0	0	0
-Mir871	82	3	1	1	81	29	93	0
-Mir872	182	72	66	164	124	65	118	68
-Mir873	0	1	0	0	0	0	0	0
-Mir874	77	45	46	39	66	36	87	43
-Mir875	0	0	0	0	0	0	0	0
-Mir876	0	0	0	0	0	0	0	0
-Mir877	6	3	4	5	7	1	11	8
-Mir878	3	0	0	0	1	5	4	0
-Mir879	3	3	1	6	1	2	1	2
-Mir880	0	0	0	0	0	1	3	0
-Mir881	14	0	0	0	8	13	29	0
-Mir882	0	0	0	0	0	0	0	0
-Mir883a	1	0	0	0	0	0	0	0
-Mir883b	0	0	0	0	0	0	0	0
-Mir9-1	0	0	0	0	0	0	0	0
-Mir9-2	0	0	0	0	0	0	0	0
-Mir9-3	0	0	0	0	0	0	0	0
-Mir92-1	32320	7428	6690	16161	24182	24855	25904	7910
-Mir92-2	766	275	195	274	524	307	655	242
-Mir92b	50	32	27	60	12	9	14	33
-Mir93	1530	647	480	1397	939	691	1194	602
-Mir96	10	0	0	0	6	1	7	0
-Mir98	542	407	354	1512	256	305	374	390
-Mir99a	1194	4059	3196	2976	937	468	1037	3708
-Mir99b	2542	10307	6673	2801	2017	1131	2339	7276
-Mira	0	0	0	0	0	0	0	0
-Mirg	565	164	166	414	234	65	147	185
-Mirlet7a-1	83	29	24	89	58	36	68	32
-Mirlet7a-2	35	12	12	37	17	15	18	12
-Mirlet7b	1276	1343	1028	2983	786	655	812	1129
-Mirlet7c-1	74	69	51	151	41	45	50	55
-Mirlet7c-2	154	75	72	218	88	75	97	82
-Mirlet7d	2117	2083	1725	5400	1315	797	1470	1940
-Mirlet7e	114	233	160	648	76	64	85	196
-Mirlet7f-1	107	97	74	205	78	79	69	70
-Mirlet7f-2	2424	746	670	3360	1668	2325	2093	747
-Mirlet7g	7561	2760	2343	10488	4736	2670	5047	2547
-Mirlet7i	2525	3013	2408	9794	1507	2235	1991	2769
-Mllt10	22	4	4	2	4	26	10	4
-Mospd4	0	0	0	0	0	0	0	0
-Mphosph9	4	0	0	0	1	0	1	1
-Mrpl15	4	1	2	1	1	4	1	2
-Mrpl48	3	2	1	0	1	1	3	0
-Msx1as	0	0	0	0	0	0	0	0
-Mtag2	0	0	0	0	0	0	0	0
-Mtf2	9	1	0	3	0	1	0	1
-Mtfr1	10	0	1	1	2	22	4	0
-Mthfr	1	0	0	1	0	1	0	0
-Mtmr2	20	67	71	276	15	43	27	61
-Mug-ps1	24	0	0	0	0	7	0	0
-Mvd	0	0	0	0	0	0	0	0
-Mx1	0	0	0	0	0	0	0	0
-Mx2	0	0	0	0	0	0	0	0
-Myeov2	3	0	0	1	0	1	0	0
-Nagpa	6	1	0	1	5	7	4	0
-Ncaph2	14	1	0	0	5	16	1	2
-Ncrna00086	0	0	0	0	0	0	0	0
-Nctc1	0	1	0	0	0	0	0	0
-Ndufs6	3	0	0	1	0	5	0	1
-Neat1	21	5	7	4	1	14	7	6
-Nespas	0	1	0	0	0	0	0	0
-Ngrn	1	0	1	0	1	0	1	0
-Nip7	0	0	0	0	0	3	0	0
-Nkx2-2as	0	0	0	0	0	0	0	0
-Nkx6-2	0	1	2	1	1	0	0	0
-Nlrp1c-ps	0	0	0	0	0	0	0	0
-Nlrp5-ps	5	0	0	0	1	25	3	0
-Nnt	35	11	10	7	0	44	6	8
-Nol8	6	0	0	2	0	4	0	2
-Npff	0	0	0	0	0	0	0	0
-Nphs1as	0	0	0	0	0	0	0	0
-Npm3-ps1	0	0	0	0	0	0	0	0
-Nron	0	0	0	0	0	0	0	0
-Nt5c2	7	1	0	3	3	11	0	1
-Numb	20	4	2	6	8	30	8	2
-Nup88	3	1	1	3	0	7	0	0
-Nutf2-ps1	0	0	0	1	0	1	0	0
-Oas1b	0	0	1	0	0	2	0	0
-Oaz1-ps	5	2	6	2	11	7	4	4
-Olfr1077-ps1	0	0	0	0	0	0	0	0
-Olfr1300-ps1	0	0	0	0	0	0	0	0
-Olfr1372-ps1	0	0	0	0	0	0	0	0
-Olfr29-ps1	0	0	0	0	0	0	0	0
-Olfr421-ps1	0	0	0	0	0	0	0	0
-Olfr75-ps1	0	0	0	0	0	0	0	0
-Olfr856-ps1	0	0	0	1	0	1	0	0
-Olfr947-ps1	0	0	0	0	0	0	0	0
-Oprl1	0	0	0	0	0	0	0	0
-Orc4	1	2	0	1	1	4	0	0
-Orc6	1	1	0	0	1	1	1	0
-Osbpl1a	9	0	2	1	1	36	0	3
-Otub2	0	0	0	0	0	2	1	0
-Otx2os1	1	0	1	0	0	0	0	0
-Oxsr1	9	1	1	1	0	10	1	1
-Pafah1b1	8	3	3	2	0	16	4	4
-Parp6	8	0	2	4	0	8	2	0
-Patz1	0	0	0	2	0	0	0	0
-Pax6os1	0	0	0	0	0	0	0	0
-Pcdh11x	2	0	0	0	0	0	0	0
-Pdxk-ps	0	0	0	0	0	0	0	0
-Pea15b	0	0	0	0	0	0	0	0
-Peg13	3	0	1	1	0	4	0	2
-Peg3as	0	0	0	0	0	0	0	0
-Pex11b	4	0	0	2	0	4	0	0
-Pex16	12	0	0	1	2	7	8	0
-Pfkfb2	3	1	3	3	0	8	1	2
-Pglyrp2	12	0	0	0	0	15	0	0
-Phc1	0	0	0	0	0	1	0	0
-Phf21b	0	0	1	0	0	0	0	0
-Phxr4	0	0	0	0	0	0	0	0
-Phyhd1	5	0	0	0	1	12	2	0
-Pinc	0	1	0	1	0	0	0	1
-Pisd-ps1	0	0	0	0	0	0	0	0
-Pisd-ps2	0	0	0	1	0	0	0	0
-Pisd-ps3	4	1	1	2	0	5	2	0
-Pitpnm1	1	0	0	0	0	0	0	0
-Pknox1	6	0	0	0	2	7	1	0
-Pla2g2a	0	0	0	0	0	0	0	0
-Plcxd1	1	0	0	1	0	0	0	0
-Pldi	0	0	0	0	0	0	0	0
-Plk4	0	0	0	0	0	1	0	0
-Plscr3	1	0	1	1	1	0	0	0
-Pnpla2	10	4	1	1	1	8	5	2
-Polg2	0	0	0	0	2	2	0	0
-Ppargc1a	3	1	2	3	0	8	1	0
-Ppifos	3	0	0	2	0	6	0	4
-Ppp1r12b	0	0	2	0	0	1	0	0
-Ppp1r2-ps3	0	0	0	0	0	0	0	0
-Ppp1r2-ps7	0	0	0	0	0	0	0	0
-Ppp1r2-ps9	0	0	0	0	0	0	0	0
-Ppp2r2b	0	0	1	0	0	0	0	1
-Ppp2r3d	2	0	0	0	0	0	0	0
-Ppp4r1l-ps	2	0	0	1	0	5	0	0
-Pradc1	0	0	1	0	2	4	0	0
-Pram1	0	0	0	0	0	1	0	0
-Prl8a6	0	0	0	0	0	0	0	0
-Prmt1	5	1	0	2	0	2	0	0
-Prmt6	2	0	0	0	1	0	0	0
-Proc	28	0	0	0	2	50	3	0
-Prr18	0	0	0	0	0	0	0	0
-Prr3	0	0	0	0	0	0	0	0
-Psg-ps1	0	0	0	0	0	0	0	0
-Psmd2	19	2	0	3	0	29	3	2
-Pum2	16	1	4	2	0	26	2	1
-Pvt1	2	1	0	0	1	2	1	1
-R74862	5	0	0	1	2	3	2	2
-Rabggtb	5253	774	579	1602	3493	3501	3690	643
-Rad51d	28	8	4	12	8	28	4	0
-Ralgps2	15	1	2	0	1	10	1	0
-Ranbp3	10	0	2	0	2	5	1	1
-Rasgrp4	0	0	1	0	0	0	0	0
-Raver1-fdx1l	12	0	0	2	0	15	2	1
-Rbbp8	4	2	0	0	2	8	0	2
-Rbm18	1	2	4	0	0	3	2	0
-Rbm7	2	2	0	3	0	5	2	0
-Rbmx	48	17	9	75	33	33	12	13
-Rcbtb2	9	0	2	1	1	10	3	3
-Rchy1	4	0	1	0	1	4	1	0
-Rdh18-ps	0	0	0	0	0	2	0	0
-Rgag4	0	0	0	0	0	0	0	0
-Rhno1	0	0	2	0	0	2	0	0
-Rian	17	12	5	29	6	7	2	10
-Rit1	4	1	1	0	0	2	0	0
-Rmi1	1	1	0	1	0	4	1	0
-Rmrp	601	278	192	679	452	220	484	272
-Rmst	1	1	5	0	0	1	0	2
-Rn4.5s	0	0	0	0	0	0	0	0
-Rn45s	126292	30052	33600	12266	20627	87267	20102	30198
-Rnf126	2	1	0	0	1	1	0	0
-Rnf44	32	2	2	2	0	46	4	0
-Rnu11	104	8	12	30	11	116	8	8
-Rnu12	93	8	8	11	5	66	13	8
-Rnu6	0	0	0	0	0	0	0	0
-Rnu7	0	0	0	0	0	0	0	0
-Rnu73b	18	2	3	3	2	8	5	3
-Rpl22	14	2	0	4	0	14	4	2
-Rplp2-ps1	0	0	0	0	0	1	0	1
-Rpph1	125	10	15	40	48	103	74	15
-Rprl1	0	0	0	0	0	0	0	0
-Rprl2	0	0	0	0	0	0	0	0
-Rprl3	5	1	1	0	0	0	1	0
-Rps15a-ps4	0	0	0	0	0	0	0	0
-Rps15a-ps6	0	0	0	0	0	0	0	0
-Rps19-ps3	0	0	0	0	0	0	0	0
-Rps27	1	0	0	0	0	0	2	0
-Rps4y2	0	0	0	0	1	1	0	0
-Rreb1	46	3	4	9	3	42	4	2
-Rtel1	1	0	1	0	0	2	0	0
-Rubie	0	0	0	0	0	0	0	0
-Runx2	0	3	2	5	3	0	1	4
-Samd7	0	0	0	1	0	0	0	0
-Sapcd1	0	1	0	0	0	0	0	0
-Scarna10	7	0	2	5	3	4	1	1
-Scarna13	4	1	0	0	0	2	3	0
-Scarna17	2377	331	306	398	1752	1971	1752	337
-Scarna2	9	2	0	8	0	6	5	2
-Scarna3a	272	148	109	300	196	337	243	137
-Scarna3b	525	146	134	452	386	589	431	121
-Scarna6	589	90	88	224	500	317	495	95
-Scarna8	0	0	1	2	2	1	3	0
-Scarna9	21	10	5	3	7	8	8	5
-Scgb2b23-ps	0	0	0	0	0	0	0	0
-Schip1	0	6	6	1	0	1	0	3
-Scnn1b	0	20	5	11	0	0	0	9
-Sec14l1	0	1	0	2	0	0	0	1
-Sec16b	22	0	0	1	0	31	3	0
-Sec23b	1	1	0	0	0	5	0	0
-Sema6c	0	0	0	0	3	0	0	0
-Senp2	3	0	0	0	0	5	0	0
-Serp2	0	0	2	0	0	0	0	1
-Serpina3h	0	0	0	0	0	0	0	0
-Serpina4-ps1	145	0	0	0	19	117	14	0
-Sfpq	11	3	3	2	0	20	2	1
-Sgsm1	0	0	0	0	2	2	0	0
-Sh2d3c	2	2	3	1	0	2	1	2
-Six3os1	0	0	0	0	0	0	0	8
-Slc12a4	3	0	2	1	1	1	0	0
-Slc22a13b-ps	0	0	0	0	0	1	0	0
-Slc25a43	0	4	0	0	0	0	0	0
-Slc25a44	22	2	1	3	3	33	11	2
-Slc2a4rg-ps	0	0	0	0	0	0	2	0
-Slc35c2	2	0	0	0	0	3	0	0
-Slfn10-ps	0	0	0	0	0	0	0	0
-Slx1b	0	0	0	0	0	3	0	0
-Smarca5-ps	0	0	0	0	0	0	0	0
-Smim4	1	0	1	0	0	0	0	1
-Smok4a	0	0	0	0	0	0	0	0
-Smpx	0	0	0	2	0	0	0	2
-Snapc4	1	0	0	1	0	7	0	0
-Snhg1	8185	2277	1889	5095	5790	6478	5840	2283
-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
-Snhg4	7	4	6	11	3	3	3	10
-Snhg5	1	3	1	2	2	0	2	2
-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
-Snhg9	5	2	0	5	0	4	2	4
-Snora15	0	0	0	0	0	0	0	0
-Snora16a	121	12	16	75	44	113	70	13
-Snora17	32	3	3	12	9	82	8	6
-Snora19	0	0	0	0	0	0	0	0
-Snora20	4	1	0	3	1	7	2	0
-Snora21	3	2	0	3	4	4	3	1
-Snora23	8	0	0	1	0	5	0	0
-Snora24	42	7	5	14	33	19	32	8
-Snora26	6	0	1	0	2	1	2	1
-Snora28	25	3	5	5	7	13	8	5
-Snora2b	1	0	0	1	0	0	0	0
-Snora3	14	0	2	5	20	13	9	6
-Snora30	0	0	0	0	0	0	0	1
-Snora31	57	38	38	36	10	81	25	35
-Snora33	2	0	0	0	0	0	0	0
-Snora34	3	2	3	2	5	7	1	3
-Snora35	0	0	0	0	0	0	0	0
-Snora36b	76	79	63	156	53	38	70	98
-Snora41	90	32	20	85	38	25	85	19
-Snora43	1	1	0	3	2	0	0	0
-Snora44	159	76	73	81	82	107	88	58
-Snora47	4	1	1	2	1	2	1	1
-Snora52	24	4	4	13	16	23	13	8
-Snora5c	0	0	0	0	0	0	0	0
-Snora61	50	10	5	23	21	24	20	11
-Snora62	5	0	0	2	0	4	6	0
-Snora64	18	0	0	5	7	15	1	1
-Snora65	24	3	6	2	11	17	14	6
-Snora68	37	10	5	48	23	38	38	14
-Snora69	6	1	0	7	4	10	3	2
-Snora70	1	0	0	0	0	1	2	0
-Snora74a	7	2	5	11	0	2	2	7
-Snora75	4	0	0	3	0	2	0	1
-Snora78	5	2	0	5	0	4	2	4
-Snora7a	30	1	4	7	2	26	9	1
-Snora81	11	0	1	5	0	3	0	2
-Snord100	197	69	56	160	134	160	155	75
-Snord104	9351	886	720	2493	5610	7452	6017	929
-Snord11	150	8	14	47	59	53	54	14
-Snord110	443	266	226	297	338	266	373	262
-Snord111	23	6	4	13	14	10	6	6
-Snord116	0	0	0	0	0	0	0	0
-Snord116l1	0	0	0	0	0	0	0	0
-Snord116l2	0	0	0	0	0	0	0	0
-Snord118	0	0	0	0	0	0	0	0
-Snord12	534	115	104	602	380	354	356	121
-Snord123	10	16	11	42	2	6	6	9
-Snord14a	0	0	0	0	0	0	0	0
-Snord14c	0	0	0	0	0	0	0	0
-Snord14d	0	0	0	0	0	0	0	0
-Snord15a	20	4	3	5	10	9	4	2
-Snord15b	63	26	16	24	24	25	34	7
-Snord16a	136	5	5	29	24	130	30	9
-Snord17	326	116	78	148	228	85	269	110
-Snord19	366	148	118	333	314	465	338	121
-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
-Snord2	914	320	248	479	582	504	625	282
-Snord22	15	9	2	19	6	6	5	7
-Snord23	28	2	0	7	4	36	6	0
-Snord32a	505	164	116	501	394	378	418	170
-Snord33	649	189	195	310	598	709	602	190
-Snord34	34	4	3	13	21	15	19	1
-Snord35a	25	8	6	7	23	39	18	5
-Snord35b	5	3	1	0	1	2	3	0
-Snord37	134	39	32	89	113	74	80	44
-Snord38a	54	9	11	37	42	34	53	15
-Snord42a	61	93	100	30	31	20	35	68
-Snord42b	227	70	66	88	229	137	195	83
-Snord43	666	121	120	542	444	504	438	140
-Snord45b	620	98	72	138	458	244	499	70
-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
-Sox2ot	0	1	0	1	0	0	0	0
-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
-Spn-ps	0	0	0	0	0	0	0	0
-Spns1	5	0	0	1	1	1	0	1
-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
-Sra1	7	0	0	0	2	4	6	0
-Srsf3	7	2	8	2	11	9	14	4
-Srsf7	1	1	0	0	0	5	0	1
-Srsf9	1	2	0	1	0	7	0	3
-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
-Stmn1-rs1	0	0	0	0	0	0	0	0
-Stoml1	0	0	0	0	0	0	0	0
-Stxbp3b	0	0	0	0	0	0	0	0
-Surf1	3	0	0	2	3	7	5	0
-Suv39h2	0	0	0	0	0	0	0	0
-Svip	1	0	2	0	0	1	0	0
-Syce2	6	0	0	0	0	19	1	0
-Sycp1-ps1	0	0	0	0	0	0	0	0
-Szrd1	40	4	0	2	16	40	4	2
-Taf1b	1	1	1	0	0	0	0	0
-Taf1d	357	53	56	156	174	341	230	54
-Tardbp	18	0	1	3	7	20	3	0
-Tbrg3	1	1	0	0	0	0	0	0
-Tcp10a	0	0	0	0	0	0	0	0
-Terc	22	1	0	0	18	10	15	0
-Thap6	2	0	2	2	1	1	0	0
-Tk2	1	2	0	2	1	1	3	0
-Tmem161b	0	0	0	0	2	2	4	0
-Tmem179b	8	0	0	0	0	8	0	0
-Tmem181b-ps	0	0	0	0	0	0	0	0
-Tmem181c-ps	0	0	0	0	0	0	0	0
-Tmem194b	0	0	1	0	1	0	0	0
-Tmem205	35	2	0	1	4	57	6	1
-Tmem41a	7	0	0	0	0	5	2	0
-Tmem51as1	1	0	0	0	0	2	0	0
-Tmem80	0	0	0	1	1	0	0	0
-Tor2a	2	0	0	0	0	11	3	0
-Tpsab1	0	0	0	0	0	0	0	0
-Trappc13	1	0	0	1	0	0	3	1
-Trim30e-ps1	0	0	0	0	0	0	0	0
-Trim52	0	0	0	0	0	0	0	0
-Trmt61b	11	0	0	0	2	5	0	0
-Trpc4	1	4	1	1	0	0	1	0
-Trpt1	2	0	0	0	0	2	0	0
-Trub2	0	0	0	0	0	0	0	0
-Tsix	0	0	0	0	0	4	0	0
-Tslp	0	0	0	1	0	0	0	0
-Tspy-ps	0	0	0	0	0	0	0	0
-Tsr2	0	0	1	0	0	2	0	0
-Tubb2a-ps2	0	0	0	0	0	0	0	0
-Tubgcp4	2	2	0	1	0	7	1	0
-Tug1	18	3	0	16	2	27	6	6
-Tyms	0	0	0	0	0	0	1	1
-Tyms-ps	0	0	0	0	0	0	0	0
-Tysnd1	2	0	0	0	1	7	3	0
-Tyw5	1	1	0	0	0	0	0	1
-U05342	20	0	1	3	3	24	3	0
-U90926	0	0	0	0	0	0	0	0
-Ube2w	3	1	2	1	1	3	1	0
-Ubl4	3	1	0	1	0	5	3	2
-Ubxn11	0	0	0	0	0	0	0	0
-Uchl1as	0	0	0	0	0	0	0	1
-Ufd1l	0	0	1	0	0	6	0	0
-Uqcc	5	0	2	1	0	8	1	1
-Vash2	0	0	0	0	0	0	0	0
-Vaultrc5	243	258	161	383	159	262	286	270
-Vax2os	0	0	0	0	0	0	0	0
-Vmn1r-ps79	0	0	0	0	0	0	0	0
-Vmn2r-ps11	0	0	0	1	0	0	0	0
-Vmn2r-ps129	0	0	0	0	0	0	0	0
-Vmn2r-ps159	0	0	0	0	0	0	0	0
-Vmn2r-ps54	0	0	1	0	0	0	0	0
-Vmn2r-ps60	0	0	0	0	0	0	0	0
-Vmn2r29	2	0	0	0	0	0	0	0
-Vps39	3	1	0	0	0	8	0	0
-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
-Wiz	10	0	1	6	1	3	3	2
-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
-Zbtb24	1	0	0	1	0	0	0	0
-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
-Zfa-ps	0	0	0	0	0	0	0	0
-Zfhx2as	0	0	0	0	0	1	0	0
-Zfp133-ps	0	0	0	0	0	0	0	0
-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
--- a/tool_dependencies.xml	Fri Apr 10 22:46:53 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,93 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="R" version="3.1.2">
-        <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="graphicsmagick" version="1.3.18">
-        <repository changeset_revision="bff3f66adff2" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="ghostscript" version="9.10">
-        <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-
-    <package name="biocbasics" version="2.14">
-        <install version="1.0">
-            <actions>
-                <action type="setup_r_environment">
-                    <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="R" version="3.1.2" />
-                    </repository>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RColorBrewer_1.1-2.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/stringr_0.6.2.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/gtools_3.4.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/gdata_2.13.3.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/bitops_1.0-6.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/caTools_1.17.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/KernSmooth_2.23-13.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/gplots_2.15.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/limma_3.22.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/edgeR_3.8.5.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BiocGenerics_0.12.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/S4Vectors_0.4.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/IRanges_2.0.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/GenomeInfoDb_1.2.4.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/XVector_0.6.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/GenomicRanges_1.18.3.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Rcpp_0.11.3.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RcppArmadillo_0.4.600.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Biobase_2.26.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/codetools_0.2-9.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/iterators_1.0.7.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/foreach_1.4.2.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/checkmate_1.5.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BBmisc_1.8.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/brew_1.0-6.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/DBI_0.3.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/digest_0.6.8.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/fail_1.2.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/RSQLite_1.0.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/base64enc_0.1-2.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/sendmailR_1.2-1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BatchJobs_1.5.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/BiocParallel_1.0.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/AnnotationDbi_1.28.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/XML_3.98-1.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/xtable_1.7-4.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/annotate_1.44.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/survival_2.37-7.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/genefilter_1.48.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/lattice_0.20-29.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/latticeExtra_0.6-26.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/locfit_1.5-9.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/geneplotter_1.44.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/plyr_1.8.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/gtable_0.1.2.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/reshape2_1.4.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/dichromat_2.0-0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/colorspace_1.2-4.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/munsell_0.4.2.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/labeling_0.3.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/scales_0.2.4.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/proto_0.3-10.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/MASS_7.3-35.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/ggplot2_1.0.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Formula_1.1-2.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/cluster_1.15.3.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/rpart_4.1-8.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/nnet_7.3-8.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/acepack_1.3-3.3.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/foreign_0.8-61.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/Hmisc_3.14-6.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/diffcount/DESeq2_1.6.3.tar.gz?raw=true</package>
-
-                    
-                </action>
-            </actions>
-        </install>
-        <readme>
-        Differential gene expression analysis
-        You may need libxml2-dev for XML to compile
-        Ubuntu has a bug with libgfortran. To fix that create a symlink like: sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib/x86_64-linux-gnu/libgfortran.so
-        </readme>
-    </package>
-</tool_dependency>