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.
[ ] Figure out what exactly edgeR does here.
[ ] Implement these steps with statsmodels.
[ ] Compare the results with the original edgeR implementation. If we're not crazily off submit a PR and add it in another if-case
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
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.