Lukas Heumos
Lukas Heumos
Yeah, smaller test datasets are also fine. We have issues with some distances failing on smaller test datasets so we had to sadly keep them a bit on the larger...
@namsaraeva don't start this one before talking to me. There are likely new versions of the datasets because scperturb got published
`ERROR: No matching distribution found for codecov>=2.0.8; extra == "dev"` codecov got removed from pypi. See discussion on scverse zulip
@emdann I'd be in favor of dropping the `subset_samples` and `subset_nhoods` parameters. Do you think that there's a reasonable place and a need somewhere to mention this though? Like maybe...
@emdann do you think that you'd have time to tackle this soonish?
@emdann let's tackle this at the hackathon, OK?
@grst what else do you think we should add? Feel free to edit my issue (hope you have the rights now - if not please ping me).
> Personally, I never made good experiences with `rpy2` -- which is one reason why I stopped using these functions in more recent projects. Instead I performed DE in R...
> I would probably use the scanpy implementation but redesign the output. IMO all tools should return a dataframe with one row per `var` with p-value and logFC. This dataframe...
> > Yup, but we also have manpower for this if you don't want to do this yourself. > > ok, even better. So implementation-wise, what would you need from...