TY - JOUR T1 - SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor JF - bioRxiv DO - 10.1101/2021.01.27.428431 SP - 2021.01.27.428431 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 Y1 - 2021/01/01 UR - http://biorxiv.org/content/early/2021/08/18/2021.01.27.428431.abstract N2 - 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. ER -