scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Add cluster_resolution_finder and cluster_decision_tree for help deciding the proper resolution
- lets umap run in parallel
- Simplify scale
- Speed up categorical regressor with numba
- Generalize tl.dendrogram function to either axis
- DensMAP support
- t-SNE optimization using scikit-learn-intelex
- Reading 10x scRNA-seq with read_10x_mtx()
- diffxpy integration
- UMAP is unreproducible between 3 Windows PCs
- Docs
- Python not yet supported