scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- pl.embedding sets uns.<field>_colors when palette=None
- Plotting categorical obs warns ImplicitModificationWarning
- Use list of identifiers for `tl.rank_genes_groups(reference=...)`
- rank_genes_groups / filter_rank_genes_groups assume non-negative log1p input
- After sc.pp.normalize_total() and log1p() there is no gene expression in UMAP plot
- Dask support
- Switch our doctest handing to pytest-doctestplus
- Faster filtering on sparse matrices
- Access to Diffusion Map methods (and other embedding methods) as Scikit-Learn style API
- Error in running scrublet
- Docs
- Python not yet supported