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scanpy

  • Description

    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.

  • Usage

    To list all executables provided by scanpy, run: $ biogrids-list scanpy Copy to clipboard

  • Usage Notes

    BioGrids scanpy is a standalone python distribution that includes:

    scanpy python-igraph leidenalg jupyterlab scanpy cnmf starcatpy scikit-misc harmonypy

    with the aliases python.scanpy and jupyterlab.scanpy.

    For a list of callable programs use the biogrids-list utility:

    $ biogrids-list scanpy

  • Installation

    Use the following command to install this title with the CLI client: $ biogrids-cli install scanpy Copy to clipboard Available operating systems: Linux 64, OS X INTEL

  • Primary Citation*

    F. A. Wolf, P. Angerer, and F. J. Theis. 2018. SCANPY: large-scale single-cell gene expression data analysis. Genome biology. 19(1): 15.


    • *Full citation information available through

  • Keywords

    scRNA-Seq Analysis

  • Default Versions

    Linux 64:  1.11.2 (961.8 MB)
    OS X INTEL:  1.11.2 (865.7 MB)

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