Question: Installing old versions of cummeRbund
gravatar for vinayjrao
12 weeks ago by
vinayjrao70 wrote:


I'm running RNA-Seq data analysis using the old tuxedo protocol, which requires cummeRbund. My current version is 2.18 (not working for me), but I want to install 2.12.1 (this version works for me). Any suggestions on how it can be done?


P.S. This question has also been asked on bioconductor support by me.

rna-seq cummerbund R • 218 views
ADD COMMENTlink modified 11 weeks ago by Biostar ♦♦ 20 • written 12 weeks ago by vinayjrao70

You should know that the old 'Tuxedo' pipeline of Tophat and Cufflinks is no longer the "advisable" tool for RNA-seq analysis. The software is deprecated/ in low maintenance and should be replaced by HISAT2, StringTie and ballgown. See this paper: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. (If you can't get access to that publication, let me know and I'll -cough- help you.) There are also other alternatives, including alignment with STAR and bbmap, or pseudo-alignment using salmon.

ADD REPLYlink written 12 weeks ago by WouterDeCoster23k

I am currently learning the new tuxedo protocol, but the current analysis is for a colleague who wanted a vague idea for now, which will be analyzed better at a later point. So, I have got the differentially expressed genes, and want to plot the results using cummeRbund, for which I need your help in installing an older version.


ADD REPLYlink written 12 weeks ago by vinayjrao70
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