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

Hi,

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?

Thanks.

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.

Thanks.

ADD REPLYlink written 12 weeks ago by vinayjrao70
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