scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- ValueError: If `root` is a string, it needs to be one of [None] not 'neoblast 1'.
- FIt-SNE integration?
- filter_rank_genes_groups in version 1.6.0 takes an extremely long time to complete
- Adjust Combat for control cells
- creating and plotting dendrograms do not see the same dendrogram
- PCA don't return `Axes`
- cell_ranger flavor of highly_variable_genes expects non-logarithmized data?
- highly deviant genes implementation
- comparing distribution of cell types per cohort per groups
- Minimum cell cutoff in sc.pl.dotplot
- Docs
- Python not yet supported