scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- scanpy.pl.stacked_violin - remove "marker label" whitespace if var_names is a list of genes
- mean expression and percentage
- Type comparison issue when using read_h5ad in backed mode
- sc.tl.dpt(adata, n_branchings=2) sometimes works sometimes doesn't
- [WIP] ICA
- Add key_added option to sc.tl.paga
- added support for individual cmaps for continous variables
- Can PDF/SVG saved figures maintain text as text for further processing?
- sc.pl.dotplot() `standard_scale='var'`: should scaling be changed?
- Gene expression color legends and gene names
- Docs
- Python not yet supported