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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.

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.

Latest release

1.4.6 2020-03-17

Functionality in external

Code design

Bug fixes

1.4.5 2019-12-30

Please install scanpy==1.4.5.post3 instead of scanpy==1.4.5.

New functionality

Code design


  • changed default solver in pca() from auto to arpack

  • changed default use_raw in score_genes() from False to None