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readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
author Jim Johnson <jj@umn.edu>
date Fri, 15 Nov 2013 13:39:14 -0600
parents da7241f92ecf
children 137aab1d9ac1
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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.