scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- rank_genes_groups logfoldchange different than seurat
- Fix paga root
- interaction with loom object
- cell_ranger HVG flavor inconsistent with 10x code
- PAGA connectivity score
- turn on the existing `n_iter=` parameter in multicore tsne
- scanpy.pp.log1p with backed h5ad produces copy error
- pl.violin will not take "hue" kwarg for seaborn?
- Can we use standard_scale in umap?
- tracksplot wrong highlight groups (no brackets)
- Docs
- Python not yet supported