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Add statsmodels or pydeseq 2 support for milopy

Open Zethson opened this issue 3 years ago • 2 comments

Our current milo implementation uses edgeR from R to make a few calculations here: https://github.com/theislab/pertpy/blob/development/pertpy/tools/_milo.py#L310 . However, we want pertpy to be a pure Python experience. Hence, we want to offer an alternative that does NOT use edgeR but instead uses statsmodels to do a very similar calculations.

  • [ ] Implement an alternative (not all of edgeR) with statsmodels.
  • [ ] Implement an alternative with pydeseq2
  • [ ] Compare the results with the original edgeR implementation.

Zethson avatar Nov 07 '22 10:11 Zethson

CC @emdann

Zethson avatar Nov 07 '22 11:11 Zethson

sounds good to try, although I am not sure how comparable results would be, and it would need custom implementation for some edgeR innards e.g. TMM normalization

emdann avatar Nov 09 '22 22:11 emdann