scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- LoweringError: Failed in nopython mode pipeline (step: nopython mode backend)
- Function `plot_scatter` is breaking with matplotlib
- Use graph coloring algorithm for a “world map” avoiding to color neighboring clusters in the same color
- Spin off read/write into it's own package?
- Scanpy Clustering
- Jackstraw implementation in scanpy?
- gene co-expression networks
- Returning cluster assignments as str conflicts with matplotlib color sequences
- Generate BioContainer images
- Dotplot where sizes are proportional to p-value and the color to log2-fold change?
- Docs
- Python not yet supported