Lukas Heumos
Lukas Heumos
I won't have the bandwidth to work on this feature for a while, but I'm open to accepting PRs from anyone interested in implementing it.
The example here: https://pertpy.readthedocs.io/en/stable/usage/tools/pertpy.tools.Distance.html#pertpy.tools.Distance.bootstrap works. Could you please provide more information on how you are running the code?
> pertpy 0.7.0 this is also not the latest version. Could you try installing the latest version with ``pip install -U pertpy`, please? I also advise you to use Python...
@aterceros is this still a problem and can we help you further?
Added a rough draft https://github.com/scverse/pertpy-tutorials/blob/main/differential_gene_expression.ipynb TODOs - [ ] Maybe make the patients as independent covariates work (leads to matrix not being full rank) - [ ] Better explain what...
I'd say that they're still relevant generally. The thing is, we had thought of decoupling the DE part from pertpy into its own package as pertpy is still a bit...
Sorry, that's on me! I'll take care of this soon. If you remove these two parameters, it should hopefully still work (on main). I also have plans to ensure that...
Ouch, I see, yeah. That's also because I moved from decoupler to scanpy pseudobulk. I'll take care of it soon!
The tutorial is fixed in https://github.com/scverse/pertpy/pull/814 It still uses decoupler (although decoupler is no longer a dependency of pertpy). I don't yet have the time to overhaul it completely. Thanks...
Thank you! We'll keep it in mind for our next big iterations in 2025. Please keep the feedback coming.