scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Custom neighbor transformers with variable neighbor count <= k fail
- Export more types
- Regressing out variables in pearson residual normalization (SCTransform)
- Support values_to_plot in pl.rank_genes_groups_matrixplot and pl.rank_genes_groups_heatmap (parity with dotplot)
- Highly Variable Genes Selection using CSC `dask`
- Exposing some functions `squidpy` uses
- `pp.regress_out` fails with to many CPU-Cores
- Add ncols parameter to pl.violin()
- 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
- Docs
- Python not yet supported