scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Integration Testing CI Test Failure on python 3.13 with prerelease dependencies
- Default legend when scaling dotplots
- Add Seurat compatibility preset
- generalize sc.tl.embedding_density() to use any 'obsm' key
- Plotting a subset of the data with a dendrogram in e.g. dotplot should retain the dendrogram ordering
- Issue with numba/pynndescent during scrublet and pp.neighbors
- Investigate IRLBA
- Column-wise `dask` `map_blocks`
- Don’t create AnnData objects with duplicate var/obs names in sc.datasets
- Remove default from sc.pp.scale’s zero_center (so it never accidentally densifies)
- Docs
- Python not yet supported