muon
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muon is a multimodal omics Python framework
**Describe the bug** One of the links for "Single-cell RNA-seq and ATAC-seq integration" tutorials, "cell-type annotation" is broken. The specific link is here: https://muon-tutorials.readthedocs.io/en/latest/single-cell-rna-atac/brain3k/2-Celltype-Annotation.ipynb **To Reproduce** Open the link in...
**Describe the bug** when I test the muon pipeline by using data of 6400cells, error happens when run 'mu.pp.neighbors(mdata, key_added='wnn')'' like : *** Error in `python': malloc(): smallbin double linked...
**Describe the bug** Hi, I'm using the muon to run the co-embedding of 280k multiome dataset and submit it to the lsf system with 40CPU+300GRAM resource. It errored with ''Segmentation...
Is there a way around this? I think the original scopen project doesn't require this. (https://github.com/CostaLab/scopen/blob/master/vignettes/epiScanpy.ipynb) ``` 02/03/2023 15:54:25, iteration: 484, violation: 0.00052132 02/03/2023 15:55:08, iteration: 485, violation: 0.00051939 02/03/2023...
Hi, Is there a plan to add a footprinting analysis module in atac so that it can visualize TF footprints like Signac and ArchR? I am pretty interested in muon...
It looks like the function ac.tl.lsi is mostly just a call to `scipy.sparse.linalg.svds`. https://github.com/scverse/muon/blob/d0e2c22896a6ea1c5617ed791ce4bf8b6ae1ab55/muon/_atac/tools.py#L52 I think this function expects that you've run `ac.pp.tfidf` beforehand, but that isn't mentioned in the...
Fixing a reference where the column "Chromosome" was being called from the features dataframe despite "chr" and "chrom" being valid inputs as well.
I got the following error when running the `tl.ica` ``` mu.tl.ica( File "/usr/local/lib/python3.12/site-packages/muon/_core/tools.py", line 1382, in ica x_ica = ica.fit_transcrotm(data.obsm[basis]) ^^^^^^^^^^^^^^^^^^ AttributeError: 'FastICA' object has no attribute 'fit_transcrotm'. Did you...
**Is your feature request related to a problem? Please describe.** It takes almost 4 seconds for muon to import, it would be nice if we could `import muon` < 1s...
Muon should test against pre-releases of upstream packages. This would help avoid situations where users install incompatible versions of libraries since muon could either pin problematic dependencies or fix the...
