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Tool: Papillon: a python alternative to plot/heatmap Galaxy RNA-seq data
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gravatar for domi84
10 months ago by
domi84 • 40
Glasgow University
domi84 • 40 wrote:

Hello, I learned how to do a RNA-seq using Galaxy, without use the terminal. But then, we you want investigate your results deeply, search/plot specific genes or make a heatmap with some selected genes you need to learn how to use R and cummeRbund.

I didn't know R very well, so I wrote a python module to plot gene expression and heatmap from Galaxy cuffdiff output. Usually python is easier to learn for a newbie.

You can install it using pip or conda-forge. Any feedback or suggestion would be appreciate.

Papillon is available here, there is a quick tutorial as well.

Best Regards

Dom
cummerbund tool heatmap rna-seq cuffdiff • 570 views
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modified 10 months ago by Jennifer Hillman Jackson ♦ 25k • written 10 months ago by domi84 • 40
1
gravatar for Jennifer Hillman Jackson
10 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If you are interested in wrapping the tool for Galaxy and having it included in the Tool Shed, this is where to start: https://galaxyproject.org/tools/

Thanks, Jen, Galaxy team
ADD COMMENT • link written 10 months ago by Jennifer Hillman Jackson ♦ 25k
1

Hi, Thanks! that's useful. I need to change a bit the module, because now is working only through a scientific IDE, but it is something doable. I hope to receive some feedback before go ahead. Thanks. Dom

ADD REPLY • link written 10 months ago by domi84 • 40
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