scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- sc.pp.regress_out() trouble importing _centered from scipy.signal.signaltools
- plotting by sc.pl.dpt_timeseries(adata) has no colors
- extend options to aggregate ranks across batches for HVG selection
- "ConvergenceWarning" in sklearn when calling ”sc.tl.rank_genes_groups“ with method='logreg'
- sc.pl.paga: does not show all groups/nodes for color dpt_pseudotime
- split.by-like function for the umap to compare gene expression between conditions
- Make default for percent_top more permissive
- sc.tl.dendrogram 'var_names' -parameter bug fix
- scanpy.tl.umap should have a `key_added` parameter
- Documentation inconsistencies and mistakes - tools / embeddings / tsne, phate, umap
- Docs
- Python not yet supported