scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Documentation for rank_genes_groups
- Plotting batches singularly
- Fix font stack
- Auto-generation of Study files for Single Cell Portal submission
- log1p warns adata.X is logged when it may not be (when other layers are logged)
- Automate figure generation for docs
- why umap showing bbknn perfectively integrated but tsne
- Should log1p edit .X inplace?
- n_components parameter for t-SNE
- rank_genes_groups "groups" argument ignored or not clearly explained
- Docs
- Python not yet supported