I have not used R in a while (about a year or so) and I wanted to analyze some Cuffdiff data I generated in Galaxy (RNAseq Tuxedo pipeline). I went to use CummeRbund and found the following message:
> install.packages("CummeRbund") Warning in install.packages : package ‘CummeRbund’ is not available (for R version 3.2.3)
When I went to the repository (http://compbio.mit.edu/cummeRbund/) it looks like it has not been updated since mid-2014. Am I missing something here? Does everyone use another program now? Looks like people are still downloading it.