scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Stacked_violin color map to mean in stead of median
- correlation between cell types and obs variables
- rank_genes_groups issues with ZScore data and filter_rank_genes_groups does not have layer option
- correlation between cell types and continuous variables stored in .obs
- _sparse_nanmean is inefficient
- sc.pl.dotplot(..., categories_order=[...]) doesn't handle not providing all categories
- Better handling of upstream releases
- Remove `paga_compare` groups argument?
- Docs for `sc.tl.filter_rank_genes_group()` missing argument descriptions
- sc.tl.score_genes use_raw = None does not default to True
- Docs
- Python not yet supported