scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- bbknn integrates multiple variables
- Subsetted adata object not behaving as expected
- Improve gene expression visualisatio non UMAP
- Order of cell plotting differs in UMAP and scatterplot
- 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
- Docs
- Python not yet supported