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save data on disk error

4

Hi, When I saved multimodal data on disk following https://muon-tutorials.readthedocs.io/en/latest/single-cell-rna-atac/pbmc10k/1-Gene-Expression-Processing.html, an error occurred: TypeError: No method has been defined for writing elements to Above error raised while writing key 'atac'...

wangjiawen2013

Drawing embedding of variables shared in multiple mods will result in an error, even if axis=-1 is set.

1

**Describe the bug** Drawing umap graphs with the same variables in multiple mods will result in errors, even if axis=-1 is set. **To Reproduce** ```python import muon as mu import...

liuzj039

- [ ] Refactor `use_obs` - [ ] Make it available for other methods - [ ] Make it more performant - [ ] GPU interface - [ ] Choose...

gtca

Fix #132

1

Hi! I've encountered an issue when running `mu.pl.scatter` (#132) , as `sc.pl.scatter()` fails when passing the color as a list, as e.g. described in scverse/scanpy#1986 To avoid this issue, my...

SarahOuologuem

Add fragment file path to a merged mudata object

1

Dear muon-team, I have converted my scATAC-seq SeuratObject to a mudata object but the information on the fragments files does not seem to be transferred. mdata.uns is empty. My object...

jolvhull

float overflow in dsb normalization

1

**Describe the bug** I ran dsb normalization with muon.prot.pp.dsb(), and I realized that the results for my data did not fully match with the results of the DSBNormalizeProtein() original implementation...

javier-marchena-hurtado

Hi! I'm getting the following error when running mu.pl.scatter() with a provided color:  When setting `color=None`, the plotting function does not fail: I also checked scanpy's `sc.pl.scatter()` and **it...

SarahOuologuem

**Describe the bug** I ran dsb normalization with muon.prot.pp.dsb() and also with the original implementation in R, with the function DSBNormalizeProtein(). The results are not the same. One possible issue...

javier-marchena-hurtado

…anpy.neighbors._connectivity.umap` Scanpy 1.10.0+ removes `scanpy.neighbors._compute_connectivites_umap`, but the required functionality is still provided by `scanpy.neighbors._connectivity.umap`, so this PR swaps those out.

milescsmith

ValueError: could not broadcast input array from shape

3

Hello, I have a dataset made of unpaired RNA/ATAC seq data. I performed PCA / nearest neighbors on each modality using a standard approach and I was going for the...

wariobrega