Scanpy – Single-Cell Analysis in Python

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.

Discuss usage on the scverse Discourse. Read the documentation. If you'd like to contribute by opening an issue or creating a pull request, please take a look at our contributing guide. If Scanpy is useful for your research, consider citing Genome Biology (2018).