scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Idents in Featureplot in Seurat outputs Idents name on top of the if Label is set to true. How do we see labels on top of scanpy UMAP plots.
- Added intercept to regress_out()
- Change default leiden clustering backend to `igraph`, and reduce default number of iterations
- Why making feature names unique instead of aggregation?
- scanpy.pl.stacked_violin - remove "marker label" whitespace if var_names is a list of genes
- mean expression and percentage
- Type comparison issue when using read_h5ad in backed mode
- sc.tl.dpt(adata, n_branchings=2) sometimes works sometimes doesn't
- [WIP] ICA
- Add key_added option to sc.tl.paga
- Docs
- Python not yet supported