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Squidpy

  • Description

    is the scverse toolkit for scalable analysis and visualization of spatial molecular data. It builds on scanpy and anndata, providing streamlined APIs for feature extraction, spatial statistics, and interactive exploration of tissue sections together with microscopy images.

  • Usage

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

  • Usage Notes

    squidpy curated in BioGrids provides:

    python.squidpy

    jupyter.squidpy

  • Installation

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

  • Primary Citation*

    G. Palla, H. Spitzer, M. Klein, D. Fischer, A. C. Schaar, L. B. Kuemmerle, S. Rybakov, I. L. Ibarra, O. Holmberg, Virshup I, M. Lotfollahi, S. Richter, and F. J. Theis. 2022. Squidpy: a scalable framework for spatial omics analysis. Nature methods. 19(2): 171-178.


    • *Full citation information available through

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