scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- adata.var.sort_index(inplace=True) does not sort adata.X
- `sc.external.pp.magic`: what is `n_jobs`'s default _really_?
- sc.pp.filter_cells does not work for pseudo counts data
- Plotting UMAP in backed mode leads to error when setting color palettes
- Computes a hierarchical clustering for the variables(genes)
- Diagonal of connectivities for diffusion maps is zero - is this intended?
- Precomputed distance matrices
- plot tSNE stratified by conditions in separate plots
- ArpackError in sc.tl.pca
- Custom transformation API (variant of scanpy.pp.normalize_total such as scanpy.pp.normalize)
- Docs
- Python not yet supported