scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- `sc.pl.stacked_violin` legend shows the group median by default, How can I show the group means instead?
- Is it possible to plot PCA for multiple samples?
- Dendrogram error - symmetry
- read_h5ad backed mode still runs out of memory on large datasets
- sc.pl.rank_genes_groups does not plot on subplot axes passed to the function
- rank_genes_groups_matrixplot does not plot logfoldchanges that are NaN as zero but a fixed >0 value.
- Multiprocess for sc.tl.pca, sc.pp.neighbors, sc.tl.leiden, and sc.tl.umap
- TypeError: bbknn() got an unexpected keyword argument 'n_trees'
- `sc.external.pp.scrublet` Key error due to internal sc.pp.filter_cells/genes
- Using groups in sc.pl.umap does not allow specification of smaller palette
- Docs
- Python not yet supported