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
- Scanpy.pl.embedding throws error when projection='3d' and all values are the same for coloring
- Implement SWNE embedding
- "batch_size" parameter doesn't work for "sc.external.pp.scanorama_integrate"
- Add `scanorama.correct_scanpy` function to `sc.external.pp`
- tsne vs umap with square root/pearson residue normalization
- `sc.pl.heatmap` (and others) should offer a means of accessing the `matplotlib.pyplot.Figure` object
- `sc.pl.stacked_violin` legend shows the group median by default, How can I show the group means instead?
- Is it possible to plot PCA for multiple samples?
- Dendrogram error - symmetry
- read_h5ad backed mode still runs out of memory on large datasets
- Docs
- Python not yet supported