Question: Running MSigDB locally *without* expression data
gravatar for Kasthuri
3.7 years ago by
United States
Kasthuri260 wrote:


I understand GSEA is typically run with an expression dataset. If I have just a list of genes, I can run compute overlaps with the MSigDB database online:

However, I am wondering if I can compute overlaps in MSigDB datasets locally through a command line for a list of genes. I want to do this because I have tons of such datasets (only genes) which I need to query for overlaps with MSigDB. Has anyone done this?


command-line msigdb • 1.1k views
ADD COMMENTlink modified 2.7 years ago by predeus1.2k • written 3.7 years ago by Kasthuri260
gravatar for predeus
2.7 years ago by
predeus1.2k wrote:

What you need is an implementation of Fisher's exact test and some sort of matching algorithm.

I've never used it in a separate tool, but you probably can apply some of the code used to calculate GO enrichments, or just write it yourself - should be pretty easy.

ADD COMMENTlink written 2.7 years ago by predeus1.2k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1135 users visited in the last hour