Danila

Hey @martinrohbeck, The explanation is rather that the axis interface of MuData objects is newer than most muon interfaces, and the latter still need to be upgraded to handle non-standard...

Hi @111kakaluote, 6400 cells should not be an issue for `mu.pp.neighbors` though it depends on the available resources of course. For instance, you can find a tutorial with CITE-seq data...

Thank you, @gabumon0. Do you encounter the same issue at the line with `mu.pp.neighbors()`? Is there any log that you might be able to share?

Thanks for this question, @lzj1769, footprinting is on our roadmap!

Hey @Feilijiang, thanks for letting us know we should take a look at the performance on large datasets! It looks like a memory-related issue but there's hardly more that I...

Is there any log associated with the segmentation fault that you could share?

Thanks for noting that, @alexlenail! It might be also worthwhile to repurpose `ac.tl.lsi()` to run both TF-IDF and SVD while adding `ac.tl.svd()`. This should also make it more intuitive for...

Hey @alexlenail, Thanks for reporting, I think this is because in the current interface the matrix is imputed by default. It also seems that scOpen's interfaces have been reworked since...

To comment on the issue title, I don't think `muon.atac.pp.scopen` writes anything on disc...

I believe imputation is performed by default via the main interface ([see here](https://github.com/CostaLab/scopen/blob/6be56fac6470e5b6ecdc5a2def25eb60ed6a1bcc/scopen/Main.py#L62)) but `scopen_dr()`, which was introduced later than the interface in `muon`, does not perform imputation. We'll upgrade...