scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Best practice for handling replicates and associated statistics
- PCA, "RuntimeWarning: divide by zero encountered in log" and wrong PCs ordering with svd_solver arpack
- Math domain error when using the Wilcoxon rank-sum
- pl.umap/tsne/draw_graph colored by principal component or diffusion component
- Tha maximal number of iterations maxit (set to 20 by the program) allowed for finding a smoothing spline with fp=s has been reached
- Linking patient data with cells
- HVG by cell_ranger flavor, n_top_genes not working
- Different results in manifold topology
- Wilcoxon rank_genes_groups math domain error (Scanpy 1.4.3)
- sc.pp.regress_out and sc.pp.highly_variable interplay
- Docs
- Python not yet supported