Boris Muzellec

Hi @redst4r, good catch, thanks for pointing out this bug! > The issue with the non-full-rank: I know it doesn't make sense to run DESeq2 with that, but an error...

Hi @jeandut and @khalilouardini, thanks for this PR! It's nice that you went all the way to even support recursive interactions like "a: b:c". I experimented a bit with your...

Thanks @jeandut for the code updates. The variable names look fine now :). ### Matrix rank We still have the rank issue with designs of the form `"~ factor1 +...

Hi @thondeboer, it is not really possible to use a custom-made design matrix with pydeseq2 as of yet, but we are currently working on it (see #213).

> @jeandut hello and happy new year! is this getting back in radar? @abearab Interaction terms were implemented in https://github.com/owkin/PyDESeq2/pull/328 and are now available as part of the 0.5.0 pre-release...

Thanks for the PR @laudmt! I think it does the trick for VST, but I have a little concern regarding the fact that providing a `fit_type` other than `None` overwrites...

Hi @laudmt, I've pushed a commit in which I implemented the solution I suggested earlier, i.e. setting two separate `fit_type` and `vst_fit_type` attributes and duplicating fields (with or without a...

Hi @grst @const-ae @emdann, is there a consensus regarding what would be most convenient? I'm assuming we want to use [formulaic](https://github.com/matthewwardrop/formulaic)? I won't have the bandwidth to implement this feature...

Hi @dguin, good catch, indeed with the recent versions there now are two attributes redundantly encoding the trend curve fit type, `self.fit_type` (set in `vst`) and `self.trend_fit_type`. We should harmonize...

Hi @wangjiawen2013! Yes, it's possible to analyse single-cell data with pydeseq2 + [decoupleR](https://decoupler-py.readthedocs.io/en/latest/index.html) and/or [scanpy](https://scanpy.readthedocs.io/en/latest/index.html). See this [decoupleR vignette](https://decoupler-py.readthedocs.io/en/latest/notebooks/pseudobulk.html) or this [youtube tutorial](https://www.youtube.com/watch?v=Ee0PQUwVH8Q).