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).
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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 - 1.4.5 2019-12-30
scanpy==1.4.5.post1 instead of
facecolor='white', useful for working in dark mode A Wolf
run neighbors on a GPU using rapids PR 850 T White
param docs from typed params P Angerer