scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
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- Issues
- feat: support for directed graphs with igraph Leiden clustering
- [Feature Request] Native Python implementation of SCTransform v2 in Scanpy
- Use new umap 0.6 pipeline in `ingest`
- `pp.neighbors` silently reuses an outdated `obsm["X_pca"]` when `use_rep` is not given
- pp.combat with a categorical covariate builds a singular design matrix and can leave the batch effect in place
- feat: add dsb norm
- Consider switch to graspologic-native for faster Leiden implementation
- Remove recipes
- Remove louvain
- perf: sample discarded counts in `downsample_counts` when keeping most of the data
- Docs
- Python not yet supported