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.
Question: generating CLS file for GSEA from Cuffdiff output
4.6 years ago by
onspotproductions • 140
onspotproductions • 140 wrote:
ADD COMMENT • link •
4.3 years ago by
BioNinja • 0
BioNinja • 0 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 COMMENT • link
Please log in to add an answer.
Powered by Biostar version 2.3.0
Traffic: 1500 users visited in the last hour