scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- 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)
- Allow scanpy.tl.pca to accept a layer argument
- sc.pl.umap not properly handling Matplotlib ax object
- StackedViolin as Seurat violin plot
- Kernel dies when using batch in highly_variable_genes()
- Docs
- Python not yet supported