spatialLIBD

The 'spatialLIBD' software tool is an R package designed for interactive exploration of spatially-resolved transcriptomics data generated with the 10x Genomics Visium platform. This tool facilitates access, visualization, and inspection of spatial gene expression data, including data-driven clusters obtained through supervised or unsupervised analyses. Users can interact with the data on their local machines or through a web application. 'spatialLIBD' contributes to interpreting spatially-resolved transcriptomics data by providing interactive visualization capabilities.

Topic

Transcriptomics;Mapping;RNA-Seq;Imaging

Detail

  • Operation: Visualisation;Quantification;Gene expression profiling

  • Software interface: Library

  • Language: R

  • License: Artistic License 2.0

  • Cost: Free

  • Version name: 1.14.1

  • Credit: The Lieber Institute for Brain Development, National Institutes of Health, the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation.

  • Input: -

  • Output: -

  • Contact: Leonardo Collado-Torres lcolladotor@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data.
  • Pardo B, Spangler A, Weber LM, Page SC, Hicks SC, Jaffe AE, Martinowich K, Maynard KR, Collado-Torres L. spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data. BMC Genomics. 2022 Jun 10;23(1):434. doi: 10.1186/s12864-022-08601-w. PMID: 35689177; PMCID: PMC9188087.
  • https://doi.org/10.1186/s12864-022-08601-w
  • PMID: 35689177
  • PMC: PMC9188087

Download and documentation

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