scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- sc.tl.rank_genes_groups: reference argument is ignored
- sc.tl.dendrogram doesn't use var_names
- Reproducibility with normalize_total
- dotplot cannot set gene_symbols
- pp.neighbors returns edgeless graph for n_neighbors=1
- What does y-axis in differential gene expression plot signify?
- Common plotting library for the Scanpy ecosystem
- Public function for accessing category colors
- gex_only=True defaults in sc.read_10x_h5
- sc.pp.combat runtime/out of memory
- Docs
- Python not yet supported