scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Faster filtering on sparse matrices
- Access to Diffusion Map methods (and other embedding methods) as Scikit-Learn style API
- Error in running scrublet
- cluster cells within groups when plotting with scanpy.pl.heatmap()
- ingest confidence thresholding
- Add scran nomalisation into scanpy
- t-SNE optimization using scikit-learn-intelex
- scale function(_get_mean_var) updated for dense array, speedup upto ~4.65x
- Multibatchnorm / between library batch normalization
- Benchmark dask
- Docs
- Python not yet supported