scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Neighbors: _connected_components is only set for sparse data
- New colour palette?
- Incorrect dpt on dense toggle-switch
- sc.tl.rank_genes_groups truncates gene ids to 50 bytes/char
- Find gene symbols exist only in .raw attribute
- sc.pl.paga: TypeError: paga() got an unexpected keyword argument 'ncols'
- paga inconsistency with plotting functions
- Implement sc.get.summarized_expression_df
- Cell selection based on simultaneous expression (co-expression)
- Allow seaborn color map strings
- Docs
- Python not yet supported