scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- potential bug with gene_symbols with pl.umap
- Change the sc.pl.paga edge color
- sc.tl.embedding_density errors when a category has one observation
- dendogram by genes in scanpy.pl.dotplot()
- logFC becomes negative and disappear for the top ranked genes when use_raw=False
- `sc.pp.neighbors` uses the default value of `n_comps` in `sc.pp.pca` instead of `n_pcs` in `sc.pp.neighbors` when `X_pca ` is not precomputed
- question about diffmap specifics
- missing arg in docs for scanpy embedding
- sc.pl.violin doesn't return `ax` when it says it should
- `test_plotting.py` imports scrublet, shall be moved?
- Docs
- Python not yet supported