scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- docs: add inline example plot to sc.pl.rank_genes_groups_violin
- docs: add inline example plot to sc.pl.correlation_matrix
- 1.10 deprecation: `use_highly_variable` parameter
- New scanpy 2.0 optional dependency extra
- feat: create `scanpy2` extra for dependencies
- Integration Testing CI Test Failure on python 3.13 with prerelease dependencies
- Integration Testing CI Test Failure on python 3.12
- modernize datasets
- perf: speed up `scanpy.get.aggregate` for sparse
- feat: allow exponentiation post agg for log-fold-change in `rank_genes_groups`
- Docs
- Python not yet supported