Header

UZH-Logo

Maintenance Infos

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


Righelli, Dario; Weber, Lukas M; Crowell, Helena L; Pardo, Brenda; Collado-Torres, Leonardo; Ghazanfar, Shila; Lun, Aaron T L; Hicks, Stephanie C; Risso, Davide (2022). SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor. Bioinformatics, 38(11):3128-3131.

Abstract

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.

Abstract

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.

Statistics

Citations

Dimensions.ai Metrics
32 citations in Web of Science®
31 citations in Scopus®
Google Scholar™

Altmetrics

Downloads

8 downloads since deposited on 17 Feb 2023
4 downloads since 12 months
Detailed statistics

Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Institute of Molecular Life Sciences
Dewey Decimal Classification:570 Life sciences; biology
Scopus Subject Areas:Physical Sciences > Statistics and Probability
Life Sciences > Biochemistry
Life Sciences > Molecular Biology
Physical Sciences > Computer Science Applications
Physical Sciences > Computational Theory and Mathematics
Physical Sciences > Computational Mathematics
Language:English
Date:26 May 2022
Deposited On:17 Feb 2023 12:48
Last Modified:28 Jun 2024 01:42
Publisher:Oxford University Press
ISSN:1367-4803
OA Status:Hybrid
Free access at:PubMed ID. An embargo period may apply.
Publisher DOI:https://doi.org/10.1093/bioinformatics/btac299
PubMed ID:35482478
  • Content: Published Version
  • Language: English
  • Licence: Creative Commons: Attribution 4.0 International (CC BY 4.0)