Question: generating CLS file for GSEA from Cuffdiff output
0
gravatar for onspotproductions
4.6 years ago by
United States
onspotproductions140 wrote:

I have differential expression data generated from cuffdiff that we would like to perform GSEA & GSVA on. I am unsure how to generate a CLS file for use with either of these toolsets. I plan to uses databases from msigDB and gseapy.

ADD COMMENTlink modified 4.3 years ago by BioNinja0 • written 4.6 years ago by onspotproductions140
0
gravatar for BioNinja
4.3 years ago by
BioNinja0
BioNinja0 wrote:

If you plan to use gseapy, the fastest way is that you can assign a python list object to the parameter cls inside python console like this:

class_verctor = ['KO','KO','KO','WT','WT','WT']

You can see some examples here: http://pythonhosted.org/gseapy/gseapy_example.html

ADD COMMENTlink modified 4.3 years ago by geek_y11k • written 4.3 years ago by BioNinja0
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