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
- sc.external.exporting.cellbrowser: cellbrowser_raw_data\sample_colors.tsv does not exist, skipping it An exception has occurred, use %tb to see the full traceback.
- `rank_genes_groups(method="t-test", mean_in_log_space=False)` runs the t-test on exponentiated values
- fix: run t-test on log values regardless of `mean_in_log_space`
- The `.uns` output for `scanpy.pp.highly_variable_genes` is not documented
- `anndata.acc` replacement for functions taking `obsm`, `layer`, …
- fix: handle scalar string groups in ranked-gene plots
- fix: keep FlyBase gene nan when reading 10x mtx
- feat: add configurable columns to PAGA plots
- sc.pl.paga raises TypeError when cax is passed with multiple colors
- fix: sc.pl.paga cax handling with multiple colors
- Docs
- Python not yet supported