scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- An advice for color palette in adata.uns
- Potential error in scanpy.tl.rank_genes_groups?
- Can't implicitly convert non-string objects to strings. Bug about tl.filter_rank_genes_groups and tl.rank_genes_groups
- n_components parameter for sc.tl.tsne
- change location of add_totals values for sc.pl.dotplot
- Always add 'use_rep' for uns["neighbors"]["params"]
- Different outputs between heatmap plot and matrix expression values
- obs. vs. obs for all grouped plots using `BasePlot`
- New plot function to draw the relations between 2 categorical adata.obs variables?
- Stacked barplot
- Docs
- Python not yet supported