pertpy
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Add statsmodels or pydeseq 2 support for milopy
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.
CC @emdann
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