scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- fix(experimental.pp.hvg): scope per-batch clip threshold in pearson_residuals HVG
- fix: anchor sc.pl.scatter colorbar to user-supplied ax
- feat: allow precomputed connectivities in neighbors
- Investigate our neighbors algorithm choice
- wilcoxon DE, vs_all_perturbed
- Investigate `networkit` (for `leiden` implementation)
- add backends
- fix: consistent modularity by using Weighted_Adjacency directly
- Automatically using Dask for large datasets when necessary
- Integration Testing CI Test Failure on python 3.13 with prerelease dependencies
- Docs
- Python not yet supported