scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Error when running sc.tl.rank_genes_groups
- Refactor `BasePlot` not to create a dataframe representation of the data
- Apple Silicon: Accelerate or openBLAS for Numpy
- Remove "n_genes_by_{expr_type}" typo from variable-level qc metrics docs
- 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
- Docs
- Python not yet supported