generating CLS file for GSEA from Cuffdiff output
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.
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BioNinja •
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onspotproductions
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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
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GouthamAtla
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BioNinja •
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