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
- logFC becomes negative and disappear for the top ranked genes when use_raw=False
- `sc.pp.neighbors` uses the default value of `n_comps` in `sc.pp.pca` instead of `n_pcs` in `sc.pp.neighbors` when `X_pca ` is not precomputed
- question about diffmap specifics
- missing arg in docs for scanpy embedding
- sc.pl.violin doesn't return `ax` when it says it should
- `test_plotting.py` imports scrublet, shall be moved?
- read_10x_mtx with different prefixes for the barcodes, features and matrix files
- Scanpy neighbors bug with identical/almost identical cells.
- Add support for passing boolean columns in .obs when plotting clustermap or dendrogram.
- Document parameter "dot_color_df" for Dotplot
- Docs
- Python not yet supported