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

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

doi:10.1093/bioinformatics/btac299

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

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

Bloomberg School of Public Health

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English (US)
Pages (from-to)	3128-3131
Number of pages	4
Journal	Bioinformatics
Volume	38
Issue number	11
DOIs	https://doi.org/10.1093/bioinformatics/btac299
State	Published - Jun 1 2022

ASJC Scopus subject areas

Computational Mathematics
Molecular Biology
Biochemistry
Statistics and Probability
Computer Science Applications
Computational Theory and Mathematics

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10.1093/bioinformatics/btac299

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abstract = "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.",

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doi = "10.1093/bioinformatics/btac299",

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AU - Righelli, Dario

AU - Weber, Lukas M.

AU - Crowell, Helena L.

AU - Pardo, Brenda

AU - Collado-Torres, Leonardo

AU - Ghazanfar, Shila

AU - Lun, Aaron T.L.

AU - Hicks, Stephanie C.

AU - Risso, Davide

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AB - 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.

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

Abstract

ASJC Scopus subject areas

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