scverse / pertpy

Perturbation Analysis in the scverse ecosystem.
https://pertpy.readthedocs.io/en/latest/
MIT License
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Add statsmodels support for milopy #175

Open Zethson opened 2 years ago

Zethson commented 2 years ago

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.

Zethson commented 2 years ago

CC @emdann

emdann commented 1 year ago

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