scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- sc.pp.neighbors(..., knn=True, n_neighbors=k) does not threshold the adjacency
- Different clustering results when setting metrics = "cosine", using callable cosine function and direct cos distance input.
- sc.pl.paga_path error in dimensions of array passed to ax.imshow
- Broken Scrublet Test
- FindConservedMarkers implementaion in Scanpy
- rank genes groups errors on less than 2 cells in a category
- Investigate Array API usage in scanpy codebase
- Don't prepend `"X_"`
- Umap parallel
- pbmc68k_reduced raw counts
- Docs
- Python not yet supported