scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- NAN as gene name in sc.get.rank_genes_groups_df
- Making var_group_rotation work when swap_axes is True
- Violin plot should allow to specify gene_symbols column in .var to use
- 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?
- TypeError: expected dtype object, got 'numpy.dtype[float64]' when running scanpy on scvelo objects
- Ingest fails when features are not 100% the same for both adata objects.
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- Python not yet supported