scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Implement `sc.tl.mde`
- UMAP transform
- Scanpy does not work with with few permissions
- How to extract cells co-expressing certain genes of interest ?
- Will scanpy implement ICA?
- read_10x_mtx with different prefix
- Small multiple plots for clusters
- sc.pp.neighbors throws KeyError: diffmap_evals due to obsm concatenation
- Legends not accessible via provided axis and misplaced (scatterplot, subplots)
- Order of plotting datapoints with categorical colouring should be amended
- Docs
- Python not yet supported