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pySCENIC

  • Description

    is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

  • Usage

    To list all executables provided by pySCENIC, run: $ biogrids-list pyscenic Copy to clipboard
  • Usage Notes

    BioGrids pyscenic provides the following callable executables:

    pyscenic

    python.pyscenic

  • Installation

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

    B. V. de Sande, C. Flerin, K. Davie, M. D. Waegeneer, G. Hulselmans, S. Aibar, R. Seurinck, W. Saelens, R. Cannoodt, Q. Rouchon, T. Verbeiren, D. D. Maeyer, J. Reumers, Y. Saeys, and S. Aerts. 2020. A scalable SCENIC workflow for single-cell gene regulatory network analysis. Nature protocols. 15(7): 2247-2276.


    • *Full citation information available through

  • Keywords

    scRNA-Seq Analysis

  • Default Versions

    Linux 64:  0.12.1 (1.0 GB)
    OS X INTEL:  0.12.1 (874.3 MB)

  • Other Versions

      Linux 64:

      0.11.2 (1.0 GB)
    • OS X INTEL:

      0.11.2 (923.2 MB)
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