scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- fix: stabilize regress_out for ill-conditioned covariates
- feat: add poisson_gene_selection flavor to pp.highly_variable_genes
- feat: sample score_genes controls per gene
- fix: reject mismatched raw var names in QC metrics
- `anndata.acc` based API for `obs_df`,`var_df`
- fix: correct binary logistic marker score direction
- `calculate_qc_metrics(use_raw=True)` labels `.raw`'s matrix with `adata.var`
- sc.external.exporting.cellbrowser: cellbrowser_raw_data\sample_colors.tsv does not exist, skipping it An exception has occurred, use %tb to see the full traceback.
- sc.pl.paga raises TypeError when cax is passed with multiple colors
- fix: sc.pl.paga cax handling with multiple colors
- Docs
- Python not yet supported