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

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 dem...

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Detalles Bibliográficos
Autores principales: Righelli, Dario, Weber, Lukas M, Crowell, Helena L, Pardo, Brenda, Collado-Torres, Leonardo, Ghazanfar, Shila, Lun, Aaron T L, Hicks, Stephanie C, Risso, Davide
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9154247/
https://www.ncbi.nlm.nih.gov/pubmed/35482478
http://dx.doi.org/10.1093/bioinformatics/btac299
Descripción
Sumario: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, TENxVisiumData and ggspavis packages are available from Bioconductor. The package versions described in this manuscript are available in Bioconductor version 3.15 onwards. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.