PT  - JOURNAL ARTICLE
AU  - Dario Righelli
AU  - Lukas M. Weber
AU  - Helena L. Crowell
AU  - Brenda Pardo
AU  - Leonardo Collado-Torres
AU  - Shila Ghazanfar
AU  - Aaron T. L. Lun
AU  - Stephanie C. Hicks
AU  - Davide Risso
TI  - SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor
AID  - 10.1101/2021.01.27.428431
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.01.27.428431
4099  - http://biorxiv.org/content/early/2021/08/18/2021.01.27.428431.short
4100  - http://biorxiv.org/content/early/2021/08/18/2021.01.27.428431.full
AB  - 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{at}gmail.com, shicks19{at}jhu.eduSupplementary Information Supplementary Tables and Figures are available online.Competing Interest StatementThe authors have declared no competing interest.