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.
If Scanpy is useful for your research, consider citing Genome Biology (2018).
Follow changes in the release notes.
News - CZI grant 2019-11-14¶
Scanpy has been selected an essential open source software for science by CZI among 32 projects, along with giants such as Scipy, Numpy, Pandas, Matplotlib, scikit-learn, scikit-image/plotly, pip, jupyterhub/binder, Bioconda, Seurat, Bioconductor, and others.
Bumped version requirement of
1.5.0 release adds a lot of new functionality, much of which takes advantage of
0.7.0 - 0.7.2. Highlights of this release include support for spatial data, dedicated handling of graphs in AnnData, sparse PCA, an interface with scvi, and others.
Spatial data support