scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- PAGA plot resets colors
- SystemError: /home/conda/feedstock_root/build_artifacts/python-split_1625973859697/work/Objects/listobject.c:138: bad argument to internal function
- scanpy.tl.umap after bbknn
- Different connectivties and UMAP if using data in X or obsm
- Sublevels in legends of plots
- ValueError: b'svddc failed in l2fit when using flavor = 'seurat_v3'
- Possible enhancement: multithreaded (via numba) mann-whitney tests
- Allow users to pass inner to sc.pl.violin when multi_panel=True
- Specification of files required for `read_10x_mtx`
- sc.pl.violin doesn't work with `groupby` and `ax` passed together
- Docs
- Python not yet supported