scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- dealing with duplicated gene symbols
- sc.pp.highly_variable_genes with flavor='seurat_v3' and batch_key: conflict with documentation
- Add Shannon Component Analysis
- bug fix: hue in sc.pl.violin
- ingest after bbknn produces poor results
- correlation between celltypes and age
- dotplot with x axis being one variable and y axis being another variable
- Plotting error after creating new category: 'Float64Index' object has no attribute 'add_categories'
- Rasterisation/vector_friendly not always working
- categories_order of sc.pl.tracksplot does not work
- Docs
- Python not yet supported