scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- rank_genes_groups refactoring
- batch_key of highly_variable_genes not working
- subsetting / subclustering, use raw
- n_bins not respected in highly_variable_genes(..., flavour='cell_ranger')
- sc.pp.recipe_zheng17 function is different from the Zheng et al. (2017) paper
- Scatter plots coloring when a gene in the column specified by `gene_symbols=` corresponds to multiple entries
- sc.pl.stacked_violin overplotting of y-axis scale
- Add layer support to sc.tl.score_genes
- Use multiple groups as reference when testing genes
- Ingest Concat
- Docs
- Python not yet supported