Create a cistopic object using ATAC-seq count matrix (peak by cell)?

aertslab / pycisTopic

pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.

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Create a cistopic object using ATAC-seq count matrix (peak by cell)? #101

Open CYorick opened 8 months ago

CYorick commented 8 months ago

Hi, it seems to me that we can only create a cistopic object using a matrix containing cell names as column names, regions as row names. If I already have a matrix, cell names as column and peaks as row, how can I create a cistopic object and do the scenicplus analysis?

Thanks!

SeppeDeWinter commented 8 months ago

Hi @CYorick

I'm not sure I'm entirely understanding your question...

Could you clarify a bit more please?

Seppe

TingTingShao commented 4 months ago

I think he/she is referring to the tutorial Using pycisTopic on simulated melanoma data.