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 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).