scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- RuntimeError: libpng signaled error
- Subsample by observations grouping
- sc.pl.paga
- Switch t-SNE in scanpy to openTSNE
- Fix diffmap plotting
- Improve documentation for violin plot to illustrate per-gene usage – violin(adata.T, 'gene_property')
- Investigate Dask for speeding up Zheng17
- Introduce GLM-PCA to scanpy.external
- Reading 10x scRNA-seq with read_10x_mtx()
- diffxpy integration
- Docs
- Python not yet supported