scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Store predefined group colors as dict?
- Issue with regress_out() and tagging rather than removing highly variable genes?
- sc.tl.rank_genes_groups to rank only specific genes of interest?
- sc.pl.heatmap show the wrong scale
- `score_genes` does not work on a dataset loaded with `backed="r+"`
- TypeError when using the exporting.spring_project function
- rank_genes_groups one- or two-sided test
- Cluster cols and rows of stacked violin
- Finding a better home for cluster centroids (i.e. 🚫_tmp_cluster_pos)
- Caching in Scanpy
- Docs
- Python not yet supported