scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Plotting colors from obsm
- ~ 35.63% faster filtering
- faster reading of h5ad file (~18X faster)
- Nan values after running sc.tl.filter_rank_genes_groups and plotting
- "Interactive" Dotplot version: check for available var_names
- Allow both 'on data' legend together with legend on righ-hand side of plot
- Rethink group IDs in rank_genes_groups
- UMAP ignores n_components when initial position is paga
- Bugs with pypairs functions
- legend position export
- Docs
- Python not yet supported