Chris Rands

This is a simple python 3 vs. python 2 issue, is has been fixed in this repo, would someone (@rossant ?) be able to tag a new release here on...

@rossant Thanks for the response, are you not maintaining it because better tools are available or because you are too busy?

Ok thanks, I didn't see those previous threads. Yes I think there are two different points. First, the viz part, which you've already covered (the mudata way looks good to...

Thanks. Maybe I'm not explaining myself well, I would like this to work:`upsetplot.from_contents({"A": [1,2,1], "B": [1,3,4]})`, which raises: `ValueError: Got duplicate ids in a category`. (In the same way that...

Thanks, I prefer the embedded `nbviewer` link, but can you revert the other formatting changes?

Docker works for me, but instructions to run on `singularity` would be nice (avoiding the need for sudo), i got this far... ``` singularity pull docker://gregoryschwartz/too-many-cells:0.2.2.0 singularity build too-many-cells docker://gregoryschwartz/too-many-cells:0.2.2.0...

Did anyone resolve this? There seem to be multiple related issues here: https://github.com/mojaveazure/seurat-disk/issues/47 https://github.com/mojaveazure/seurat-disk/issues/53 https://github.com/mojaveazure/seurat-disk/issues/64 https://github.com/mojaveazure/seurat-disk/issues/70 and on hdf5r , https://github.com/hhoeflin/hdf5r/issues/166, and seurat https://github.com/satijalab/seurat/issues/3164 I have this error even when...

I think I found a (partial) solution, save with gzip compression and as dense matrix, e.g. `python -c "import scanpy as sc; adata = sc.read('pbmc3k_final.h5ad'); adata.write('pbmc3k_final_gzip.h5ad', compression='gzip', force_dense=True)" `. I...

Was this fixed by https://github.com/scverse/scanpy/pull/2344 ? Edit: Yes

How is the batch size determined? Did i miss a parameter? `linked` in this case contains 172 elements We can trivially pick a different linked record of course, but just...