scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- data types preventing sc.tl.rank_genes_groups from running
- Can Ingest solve some problems for dataset with batch effect?
- Exporting a PAGA to gexf format: AttributeError: 'Graph' object has no attribute 'node'
- recommended/default data type for visualisation is obscure
- scanorama corrected matrices
- Disable the "scatter" prefix in scanpy.pl.scatter
- potential bug with gene_symbols with pl.umap
- Change the sc.pl.paga edge color
- sc.tl.embedding_density errors when a category has one observation
- dendogram by genes in scanpy.pl.dotplot()
- Docs
- Python not yet supported