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Provide functionality for gene enrichment analyses

Open rmarkello opened this issue 5 years ago • 1 comments

The issue

abagen currently does a lot of leg work for going from the microarray expression data obtained via the AHBA to parcellated expression data. But, after that, things are left up to the user, and we don't have a lot of functionality (outside of some minor utilities in abagen.correct) to do anything else. It might be nice to provide some additional functionality for people interested in that sort of thing!

Proposed solution

Having approximately zero background in genetics, it seems like the "normal" thing to do with AHBA data are gene enrichment analyses. Thankfully, there's a Python toolbox for that which we could investigate integrating into abagen.

I'm also open to other suggestions for some analyses that might be fun to do with the data returned from abagen.get_expression_data()!

rmarkello avatar Sep 20 '19 19:09 rmarkello

Another potential tool: https://github.com/zqfang/GSEApy

rmarkello avatar Sep 20 '19 20:09 rmarkello