scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Make default for percent_top more permissive
- sc.tl.dendrogram 'var_names' -parameter bug fix
- scanpy.tl.umap should have a `key_added` parameter
- Documentation inconsistencies and mistakes - tools / embeddings / tsne, phate, umap
- Tools dendogram fails when using categorical obs key where not all categories have values
- Nearest neighbours
- ImplicitModificationWarning: Trying to modify attribute `._uns` of view, initializing view as actual. self.data[key] = value
- Regress_out function sets means of genes to zero
- Parallel read
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- Python not yet supported