Peak GC content quantification in ATAC module

scverse / muon

muon is a multimodal omics Python framework

https://muon.scverse.org/

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Peak GC content quantification in ATAC module #54

Open emdann opened 2 years ago

emdann commented 2 years ago

Hi there,

First of all, every time I go back to working with muon it gets better and better, so thanks for the great work!

I was wondering whether you had thought of adding a muon.atac.pp function to compute GC content of peaks. This is frequently used for peak-gene association testing (e.g. here), and as far as I am aware there is no easy functionality in python for this (I've always used addGCBias from chromVAR in R).

gtca commented 2 years ago

Thank you, @emdann!

Thanks for raising this, we plan to improve how peak sequences are operated indeed. That should include GC content. Currently, there's ac.tl.get_sequences to get a list of strings (a sequence for each peak) and one can start with calculating G and C fractions from that. (We will probably refactor things here but a similar function will still be available.)