scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Uns categorical colour maping as a dictionary
- STARsolo Matrix with Velocyto --> Anndata function
- KeyError: 1 in read_10x_mtx if genes.tsv has only one column
- Ingest won't integrate datasets of different lengths
- Add counts layer automatically
- Add graph coloring algorithm as an alternative for `palette`
- Figures related to rankings and heatmap could be transposed.
- Heatmap does not respect Ordered Categorical
- sc.pl.palettes.godsnot_64 18th colour invisible against white BG
- add multibatchPCA approach?
- Docs
- Python not yet supported