scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- allowing dotplot to use two variables in groupby as x and y axis
- rank_genes_groups_dotplot does not work when using reference and using rankby_abs, or setting; values_to_plot='logfoldchanges'
- `sc.pl.stacked_violin`, Is it also possible to add tiny y-axis scale bars to the stacked_violin(`swap_axes = True`)?
- Neighbors.compute_transitions() with error 'AnnData' object has no attribute '_connectivities'
- Gene selection plot for Pearson Residuals
- "scanpy.pl.rank_genes_groups{,_violin}" are inconsistent with gene_names assignment
- TypeError: Can't implicitly convert non-string objects to strings
- Why not give users the ability to save figures how/where they please?
- `invalid value encountered in divide` when running `pp.normalize_pearson_residuals`
- Patching scanpy for xeus
- Docs
- Python not yet supported