Anastasia Litinetskaya

Hi folks, I also had the same issue when trying to run `de.test.wald`. As @KeitaSaeki suggested, it looks like the problem was the name of the index column, i.e. in...

Hi @cchrysostomou, did you by any chance figure out how to fix this? I'm having the same issue.

Hi @Yansr3, Thanks for reporting this! Could you try installing both scarches and multigrate from github?

Hi, should be fixed after we move to decoupler (#141).

oh thanks, forgot to remove, we don't need it any more --- View entire conversation on ReviewNB

following decoupler tutorial here https://decoupler-py.readthedocs.io/en/latest/notebooks/pseudobulk.html --- View entire conversation on ReviewNB

It comes from https://decoupler-py.readthedocs.io/en/latest/generated/decoupler.get_pseudobulk.html#decoupler.get_pseudobulk params min_prop=0.2 and min_smpls=3, which filter out genes that are expressed in <20% of all cells and genes that are expressed in <3 samples --- View...

Didn't notice, thanks! will fix --- View entire conversation on ReviewNB

I'm not sure if it'd better to make these more permissive --- View entire conversation on ReviewNB

Hey @soroorh, we changed to decoupler for pseudobulk creation which filters out genes that are expressed in