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Provide functionality for gene enrichment analyses #112

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rmarkello opened this issue Sep 20, 2019 · 1 comment
Open

Provide functionality for gene enrichment analyses #112

rmarkello opened this issue Sep 20, 2019 · 1 comment
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enhancement New feature or request low priority Would be nice but definitely not urgent question Further information is requested

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@rmarkello
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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 rmarkello added enhancement New feature or request question Further information is requested low priority Would be nice but definitely not urgent labels Sep 20, 2019
@rmarkello
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Another potential tool: https://github.com/zqfang/GSEApy

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Labels
enhancement New feature or request low priority Would be nice but definitely not urgent question Further information is requested
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