scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Set n_pcs when use_rep is specified in sc.pp.neighbors
- DE analysis and filter_rank_genes_groups
- Workflow for merging bug fixes
- Random test failure of `test_plotting.py::test_paga`
- Allow using arbitrary vectors in plotting (not only `obs` columns)
- Matrixplot alternative group statistics
- More hierarchical API
- Specify var subsets for stats testing
- Making var_group_rotation work when swap_axes is True
- Violin plot should allow to specify gene_symbols column in .var to use
- Docs
- Python not yet supported