scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Rank refactor 1
- wilcoxon DE, vs_all_perturbed
- Investigate `networkit` (for `leiden` implementation)
- add backends
- fix: consistent modularity by using Weighted_Adjacency directly
- Scrublet failure using `batch_key`
- race condition breaks parallel run of `sc.datasets` functions (e.g. in tests)
- Automatically using Dask for large datasets when necessary
- Integration Testing CI Test Failure on python 3.13 with prerelease dependencies
- `base` without `X_`
- Docs
- Python not yet supported