scanpy

Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.

More Information

For more information visit the scanpy website.

Available Versions

These versions of scanpy are available on the BEAR systems (BlueBEAR and BEAR Cloud VMs). These will be retained in accordance with our Applications Support and Retention Policy.