scanpy
https://github.com/scverse/scanpy
Python
Single-cell analysis in Python. Scales to >1M cells.
Triage Issues!
When you volunteer to triage issues, you'll receive an email each day with a link to an open issue that needs help in this project. You'll also receive instructions on how to triage issues.
Triage Docs!
Receive a documented method or class from your favorite GitHub repos in your inbox every day. If you're really pro, receive undocumented methods or classes and supercharge your commit history.
Python not yet supported1 Subscribers
Add a CodeTriage badge to scanpy
Help out
- Issues
- `highly_variable_genes` with `batch_key` and `subset=True` keeps the wrong genes when `n_top_genes` is not set
- fix: keep gene order in batched `highly_variable_genes` without `n_top_genes`
- fix: reject mismatched raw var names in QC metrics
- `anndata.acc` based API for `obs_df`,`var_df`
- don’t return dicts
- feat: switch to `use` and `out`
- fix: correct binary logistic marker score direction
- `calculate_qc_metrics(use_raw=True)` labels `.raw`'s matrix with `adata.var`
- docs: document the `adata.uns['hvg']` output of `pp.highly_variable_genes`
- Docs
- Python not yet supported