scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- sc.pl.paga_path: n_avg>1 messes up legend
- sc.tl.paga_expression_entropies(adata)
- Additional functionality
- Replace set_figure_params(transparent=True) with set_figure_params(facecolor=(0,0,0,0))
- paga colorbar
- Flaws with current approaches for normalization, PCA, and feature selection?
- sc.pl.rank_genes_groups_heatmap runs slowly
- Take n_bins into account for the cell_ranger flavor of highly_variable_genes
- sc.pl.paga_compare fails when color is different than groups parameter of sc.tl.paga
- Show scatterplots with colorbar side-by-side
- Docs
- Python not yet supported