scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Scanpy’s tests should prevent DeprecationWarnings and FutureWarnings
- sparse array support
- Added compressed parameter to read_10x_mtx to support STARsolo output
- Investigate annoy out-of-core
- Fix link to preprocessing recipe of Zheng et al. 2017 and typo
- (fix): correct `dtype` for `transform` in `PCAEighDaskFit.transform`
- Whether the highly variable gene selection method seurat_v3 of Scanpy is really the same as the vst method of Seurat.
- read_10x_mtx assumes mtx.gz
- Enhance Clustering Resolution Selection with Hierarchical Tree Visualization
- Add cluster_resolution_finder and cluster_decision_tree for help deciding the proper resolution
- Docs
- Python not yet supported