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Question: Is there an alternative tool to plot RNA-Seq differential expression than cummeRbund?
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gravatar for Wanderer
11 months ago by
Wanderer • 10
Wanderer • 10 wrote:

<hey guys="">

I have some results from cuffdiff to plot but I cant use the cummeRbund, is there another tool that can accomplish the same job? I already tried several times to use the cummeRbund but isnt working.

Thank you for your time!
rna-seq plot cummerbund deseq2 cuffdiff • 803 views
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modified 10 months ago by domi84 • 40 • written 11 months ago by Wanderer • 10
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gravatar for Jennifer Hillman Jackson
11 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Yes, the plots with CummeRbund are problematic right now, details: https://github.com/galaxyproject/tools-devteam/issues/340

Please see the help for using DeSeq2 and other plotting tools included in the RNA-seq tutorials here for example alternatives: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 11 months ago • written 11 months ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for domi84
10 months ago by
domi84 • 40
Glasgow University
domi84 • 40 wrote:

Hello, I recently wrote a python module to plot genes expression. It is available here. Any feedback would be appreciate. Thanks Dom
ADD COMMENT • link written 10 months ago by domi84 • 40
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