scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Automate figure generation for docs
- why umap showing bbknn perfectively integrated but tsne
- Should log1p edit .X inplace?
- n_components parameter for t-SNE
- dealing with duplicated gene symbols
- sc.pp.highly_variable_genes with flavor='seurat_v3' and batch_key: conflict with documentation
- Add Shannon Component Analysis
- ingest after bbknn produces poor results
- correlation between celltypes and age
- dotplot with x axis being one variable and y axis being another variable
- Docs
- Python not yet supported