Running cummeRbund in R Studio

This is a sample workflow for using cummeRbund to visualize output from cuffdiff in Galaxy

cummeRbund

 * a visualizer for RNAseq output from cuffdiff
 * Currently we use R Studio to run cummeRbund, however the package may soon be available in the CofC galaxy portal

Basic Workflow
1. Upload Cuffdiff output into R Studio into the "files" tab into a newly created folder (ex: Sample)

2. Rename uploaded files (until update it will be necessary to do this step in order for cummeRbund to process the data) i.e.: ...splicing_differential_expression_testing].tabular            as      splicing.diff ..._promoters_differential_expression_testing].tabular          as      promoters.diff ..._CDS_overloading_differential_expression_testing].tabular    as      CDS.diff ..._CDS.FPKM_differential_expression_testing].tabular           as      cds_exp.diff ..._CDS_FPKM_tracking].tabular                                  as      cds.fpkm_tracking ..._TSS_groups_differential_expression_testing].tabular         as      tss_group_exp.diff ..._TSS_groups_FPKM_tracking].tabular                           as      tss_groups.fpkm_tracking ..._gene_differential_expression_testing].tabular               as      gene_exp.diff ..._gene_FPKM_tracking].tabular                                 as      genes.fpkm_tracking ..._transcript_differential_expression_testing].tabular         as      isoform_exp.diff ..._transcript_FPKM_tracking].tabular                           as      isoform.fpkm_tracking

3. Now, with the folder open (Sample) and the file names changed, set the current folder as the working directory using the "More" tab

4. Start cummeRbund by inputing: > library(cummerbund)

5. Then have cummeRbund read the files by inputing: > cuff<-readCufflinks

6.

Links
http://portal.cs.cofc.edu/rstudio/

cummeRbund Manual