scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Loophole with using scaled adata for sc.tl.score_genes_cell_cycle
- ✨ Add colorblocks to baseplot similar to heatmap
- Switch away from asv
- Update ingest example. Fixes `AttributeError: 'Ingest' object has no attribute '_pca_use_hvg'`
- feat: add layer argument for sc.tl.score_genes_cell_cycle
- Enhance scanpy.tl.rank_gene_groups with additional filters (min_pct, etc.,)
- sc.tl.dendrogram no longer(?) works in backed mode
- Switch dendrogram implementation to aggregate
- Less hacky plotting classes
- rank_genes_groups fails to account for multiple comparsions when multiple groups are provided.
- Docs
- Python not yet supported