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

Dario Righelli; Lukas M. Weber; Helena Lucia Crowell; Brenda Pardo; Leonardo Collado‐Torres; Shila Ghazanfar; Aaron T. L. Lun; Stephanie C. Hicks; Davide Risso

doi:10.1093/bioinformatics/btac299

BioinformaticsBioinformaticsApr 25, 2022

Peer-reviewed journal article

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

Dario Righelli iD, Lukas M. Weber iD, Helena Lucia Crowell iD, Brenda Pardo iD, Leonardo Collado‐Torres iD, Shila Ghazanfar iD, Aaron T. L. Lun iD, Stephanie C. Hicks iD, Davide Risso iD

Abstract

SummarySpatialExperiment 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 ImplementationThe SpatialExperiment, STexampleData, TENxVisiumData, and ggspavis packages are available from Bioconductor. The package versions described in this manuscript are available in Bioconductor version 3.15 onwards. Contactrisso.davide@gmail.com, shicks19@jhu.edu Supplementary InformationSupplementary Tables and Figures are available online.

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