Mercurial > repos > jjohnson > cummerbund

diff README @ 15:2d7eee38ab5b

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
author Jim Johnson <jj@umn.edu>
date Fri, 08 Nov 2013 13:28:44 -0600
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Fri Nov 08 13:28:44 2013 -0600
@@ -0,0 +1,20 @@
+CummeRbund is an R package that is designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output.
+( http://compbio.mit.edu/cummeRbund/ )  
+
+
+Prerequisites for installing cumme=Rbund:
+The linux package: libxml2-dev
+In ubuntu:   sudo apt-get install libxml2-dev
+
+R package: ggplot2
+   install.packages("ggplot2",dependencies = TRUE)
+
+To install cummeRbund on your R server, follow the directions in:
+( http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html )
+   source("http://bioconductor.org/biocLite.R")
+   biocLite("cummeRbund")
+
+This galaxy tool package includes a replacement variation of the cuffdiff wrapper that will generate an output that can be used directly in cummeRbund.
+
+
+