scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- PCA analysis doesn't look correct after upgrading
- scanpy.pp.filter_genes should have a batch key option
- Problem at reproducibility of UMAP / leiden
- Violin plot doesn't have option to return figure and doesn't check if the paths is an absolute path
- Is it possible to test for bimodality in scanpy?
- update documentation for scanpy.pl.rank_genes_group
- sc.pl.paga_path: TypeError: float() argument must be a string or a number, not 'csr_matrix'
- sc.tl.rank_genes_groups assumes the data is log(x+1) transformed
- sc.tl.rank_genes_groups: reference argument is ignored
- sc.tl.dendrogram doesn't use var_names
- Docs
- Python not yet supported