BMC Genomics (Jun 2022)

spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

  • Brenda Pardo,
  • Abby Spangler,
  • Lukas M. Weber,
  • Stephanie C. Page,
  • Stephanie C. Hicks,
  • Andrew E. Jaffe,
  • Keri Martinowich,
  • Kristen R. Maynard,
  • Leonardo Collado-Torres

DOI
https://doi.org/10.1186/s12864-022-08601-w
Journal volume & issue
Vol. 23, no. 1
pp. 1 – 5

Abstract

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Abstract Background Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. Incorporating the precise spatial mapping of gene activity advances our understanding of intact tissue-specific biological processes. In order to interpret these novel spatial data types, interactive visualization tools are necessary. Results We describe spatialLIBD, an R/Bioconductor package to interactively explore spatially-resolved transcriptomics data generated with the 10x Genomics Visium platform. The package contains functions to interactively access, visualize, and inspect the observed spatial gene expression data and data-driven clusters identified with supervised or unsupervised analyses, either on the user’s computer or through a web application. Conclusions spatialLIBD is available at https://bioconductor.org/packages/spatialLIBD . It is fully compatible with SpatialExperiment and the Bioconductor ecosystem. Its functionality facilitates analyzing and interactively exploring spatially-resolved data from the Visium platform.

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