search

scverse / pertpy

Perturbation Analysis in the scverse ecosystem.
https://pertpy.readthedocs.io/en/latest/
MIT License
133 stars 21 forks source link

pertpy_scCODA for scATAC-dataset? #285

Closed ronghai-li closed 1 year ago

ronghai-li commented 1 year ago

Description of feature

hey,thanks your all do for this beautiful package!

i am a beginner,i have some scATAC-dataset from difference groups, i want to try to do celltype Compositional analysis use scCODA;

1.I want to know if pertpy_scCODA can use for scATAC-dataset;

2.and how Translating from ArchR proj to Anndata,it is better if you can give a sample;

thanks all

Zethson commented 1 year ago

Hi,

  1. If you have labeled clusters - yes. I don't see why not. CC @johannesostner
  2. This is the concern of ArchR people. Please ask your question there.

Cheers

johannesostner commented 1 year ago

Yes, scCODA is suitable for all kinds of high-throuput sequencing data. I don't see a reason why you shouldn't use it for scATAC data, as long as you have some clustering labels. scATAC also has limited library size, so the data characteristics we addressed with scCODA should remain.