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
- using `adata.var_names` in `sc.get.obs_df`
- How to define customize legend order with scanpy (sc.pl.umap)?
- write anndata failed, pearson_residuals_df header message is too large
- Call `numba.set_num_threads` when `n_jobs` is specified (e.g. in `scanpy.tl.rank_genes_group`)
- scRNA-seq CRISPR data: sc.read_10x_h5 does not include guide sequence in the count matrix and .var
- Leiden, Louvain with Katana Graph
- Issue with sanitize_anndata() in plotting functions with subsets of anndata objects are passed.
- Imputation methods
- How to score cluster for presence of marker genes?
- Tracking operations performed on AnnData objects
- Docs
- Python not yet supported