scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Combat will return all NaNs in adata.X if one of the batches contains only 1 cell
- Trace back Scanpy version from h5ad file
- sc.pl.paga: TypeError: paga() got an unexpected keyword argument 'ncols'
- paga inconsistency with plotting functions
- UMAP to received pre-computer KNN graph when method=‘rapids’
- pip install scanpy[rapids] fails as cuML requirement cannot be met
- Implement sc.get.summarized_expression_df
- Cell selection based on simultaneous expression (co-expression)
- Inline example plots in docs
- Allow seaborn color map strings
- Docs
- Python not yet supported