scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Install Issue: AttributeError: module 'igraph' has no attribute 'VertexClustering'
- Issues with ingest
- More flexible umap
- Change dotplot labels from EnsemblID to geneID
- sc.tl.rank_gens_groups pts
- f"Values {list(not_found)}, from {list(indexer)}, " "are not valid obs/ var names or indices."
- Bug with pie colors in sc.pl.scanpy
- correlation between two adata objects
- Show median bars in Violin plots
- Domino plot/cell information in dotplot
- Docs
- Python not yet supported