scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Allow users to pass inner to sc.pl.violin when multi_panel=True
- Specification of files required for `read_10x_mtx`
- sc.pl.violin doesn't work with `groupby` and `ax` passed together
- Rotate genes in pl.rank_genes_groups?
- Compute UMAP from pre-existing distance matrix
- Bug on scanpy, sc.pp.neighbors function
- Store multiple Umap Coordinates
- Error when repeating the tutorial for diffusion map in v1.9.1 scanpy
- Enable matplotlib legend loc values for embeddings
- sc.pl.umap(colors=['cell_type', 'other'], legend_loc=['on data', 'right margin'])
- Docs
- Python not yet supported