scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Faster filtering of sparce matrix
- missing var_names in BasePlot
- feature selection method using pearson residuals discrepancies
- Set multiple roots in tree layout
- Neighbors: _connected_components is only set for sparse data
- New colour palette?
- Incorrect dpt on dense toggle-switch
- sc.tl.rank_genes_groups truncates gene ids to 50 bytes/char
- Find gene symbols exist only in .raw attribute
- Passing a RandomState instance can cause failures to save
- Docs
- Python not yet supported