scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Precomputed distance matrices
- ArpackError in sc.tl.pca
- Custom transformation API (variant of scanpy.pp.normalize_total such as scanpy.pp.normalize)
- Allow scanpy.tl.pca to accept a layer argument
- sc.pl.umap not properly handling Matplotlib ax object
- StackedViolin as Seurat violin plot
- Kernel dies when using batch in highly_variable_genes()
- Broken test: `TestPreprocessingDistributed::test_normalize_per_cell[dask]`
- Add a ``batch_key`` to ``sc.pp.scale()``
- key_added parameter for bbknn
- Docs
- Python not yet supported