scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- fix: regress_out for more threads than 64
- sc.pl.dotplot is surprisingly ineffective for subsets of data
- performance: Refactor BasePlot & subclasses to copy less
- Add TAU as an optional clustering method in Scanpy
- [RFC] Refactoring Scanpy's Numba Backend: C-Style Kernel Layer & Biology-Optimized Sparse Matrices
- perf: try out new cliping numba kernel
- sc.pp.scale changes adata.raw.X
- Unexpected number of non-zero distances when running `sc.pp.neighbors` with `transformer="pynndescent"`
- `scanpy.external.pp.harmony_integrate` incompatible with newly updated `harmonypy>=0.1.0`
- Improve flexibility of `sc.pp.scrublet()`
- Docs
- Python not yet supported