scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- regress_out polynomial effect
- umap for one gene split by condition
- how does sc.queries.enrich handle up- and down-regulated genes
- repeating genes in pl.rank_genes_groups_heatmap
- why cannot set the specific color?
- Ingest fails when features are not 100% the same for both adata objects.
- bbknn integrates multiple variables
- Subsetted adata object not behaving as expected
- Improve gene expression visualisatio non UMAP
- Order of cell plotting differs in UMAP and scatterplot
- Docs
- Python not yet supported