scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Zoomed out PAGA output
- Remove `sc.external`
- Enhancement of Parameter Descriptions in MatrixPlot Class Documentation
- Plotting config files
- Unify `method`/`flavor`/`backend`/… parameters
- NMF
- Dask support for normalize_pearson_residuals, highly_variable_genes(flavor='pearson_residuals')
- `pl.rank_genes_groups_violin` should be able to pass `**kwds` to `pl.violin`
- Adding format checking for sparse matrix in the function "read_v3_10x_h5"
- Pass n_iterations argument to scanpy.tl.louvain
- Docs
- Python not yet supported