scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- 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"]
- Add Poisson Gene Selection to HVG
- Mislocation of colorbar legend by `sc.pl.scatter`
- sc.read_10x_mtx KeyError: 2 The above exception was the direct cause of the following exception:
- Inconsistency of `basis` argument in plotting functions
- Custom neighbor transformers with varying neighbor count and respect `knn`
- Implementation of `sc.tl.score_genes` doesn't match reference
- Docs
- Python not yet supported