scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- 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
- Filter
- Regress out
- > [Bug] `rank_genes_groups` after `normalize_pearson_residuals`
- Fix rank_genes_groups_violin’s gene_symbols
- sc.pp.highly_variable_genes produces different hvg when run on same object with same n_genes
- Docs
- Python not yet supported