scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Add ncols parameter to pl.violin()
- sc.pl.umap does not show legend when show=False and saving figure manually
- Order of pts and pts_rest in rank_genes_groups results doesn't match other fields in adata.uns["rank_genes_groups"]
- Integration Testing CI Test Failure on python 3.13
- Add Poisson Gene Selection to HVG
- Plotting UMAP converts cell_id to category --> hinders plotting with spatialdata.plot
- Mislocation of colorbar legend by `sc.pl.scatter`
- sc.read_10x_mtx KeyError: 2 The above exception was the direct cause of the following exception:
- `read_10x_mtx()` cannot handle numerical barcodes properly (BD Rhapsody specifically)
- Remove external tests and deprecate sc.external
- Docs
- Python not yet supported