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Question: how to perform pre ranked GSEA in R?
1
gravatar for Nemo
2.7 years ago by
Nemo60
India
Nemo60 wrote:

I have a list of probes (up regulated genes) and I have a gene set (consists of several column of probes which have been already ranked based on their expression) 

Now, I want to perform  Kolmogorov-smirnov test or pre ranked GSEA. can any body help with how to do it ? you can find an example data in the following links

 

ADD COMMENTlink modified 8 months ago by predeus0 • written 2.7 years ago by Nemo60
0
gravatar for samuel collombet
2.7 years ago by
France
samuel collombet100 wrote:

Hi Nemo,

You can use the topGO package, the vignette shows example on how to do it :)

ADD COMMENTlink written 2.7 years ago by samuel collombet100
0
gravatar for predeus
8 months ago by
predeus0
United States
predeus0 wrote:

use fgsea bioconductor package.

ADD COMMENTlink written 8 months ago by predeus0
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