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SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor

By Dario Righelli, Lukas M Weber, Helena L Crowell, Brenda Pardo, Leonardo Collado-Torres, Shila Ghazanfar, Aaron TL Lun, Stephanie C Hicks, Davide Risso

Posted 27 Jan 2021
bioRxiv DOI: 10.1101/2021.01.27.428431

Summary: SpatialExperiment is a new data infrastructure for storing and accessing spatially resolved transcriptomics data, implemented within the R/Bioconductor framework, which provides advantages of modularity, interoperability, standardized operations, and comprehensive documentation. Here, we demonstrate the structure and user interface with examples from the 10x Genomics Visium and seqFISH platforms, and provide access to example datasets and visualization tools in the STexampleData, TENxVisiumData, and ggspavis packages. Availability and Implementation: The SpatialExperiment, STexampleData, and TENxVisiumData packages are available from Bioconductor. The package versions described in this manuscript are available in Bioconductor version 3.14 onwards. The ggspavis package is available from GitHub and has been submitted to Bioconductor. Contact: risso.davide@gmail.com, shicks19@jhu.edu Supplementary Information: Supplementary Tables and Figures are available online.

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