scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Inconsistency of `basis` argument in plotting functions
- Custom neighbor transformers with varying neighbor count and respect `knn`
- Implementation of `sc.tl.score_genes` doesn't match reference
- Add values_to_plot support to matrixplot and heatmap (issue #3842)
- chore(deps): bump actions/upload-artifact from 5 to 6
- Recommended order for sc.pp.filter_genes and sc.pp.normalize_total in preprocessing pipeline
- Error when running sc.tl.rank_genes_groups
- Refactor `BasePlot` not to create a dataframe representation of the data
- Apple Silicon: Accelerate or openBLAS for Numpy
- Remove "n_genes_by_{expr_type}" typo from variable-level qc metrics docs
- Docs
- Python not yet supported