scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- Dotplot where sizes are proportional to p-value and the color to log2-fold change?
- leiden and umap not reproducible on different CPUs
- counts_per_cell has no effect on pp.normalize_per_cell(adata)
- Interest in HTO/ADT demultiplexing and analysis?
- support for weighted sampled data to rank genes and plot (dot, violin…
- Any interest in getting SCTransform up on Scanpy?
- leiden alg with igraph flavor causes out of bounds freezing
- Switch t-SNE implementation to openTSNE
- Docs
- Python not yet supported