scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- UMAP ignores n_components when initial position is paga
- Bugs with pypairs functions
- legend position export
- Visualizing Standalone Dendrogram and Merging Similar Nodes
- Regressing out genes
- PAGA plotting clips edges
- Allow plotting heatmap with smoothed expressions per cluster
- Use simplified dendrogram for speed
- add restrict_to to sc.pl.umap function?
- Allow selection of layer/ raw for methods that use X
- Docs
- Python not yet supported