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

[CYorick]

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]

Hi @CYorick

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

Could you clarify a bit more please?

Seppe

[TingTingShao]

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