Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 May 26;38(11):3128-3131.
doi: 10.1093/bioinformatics/btac299.

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

Dario Righelli  1 , Lukas M Weber  2 , Helena L Crowell  3   4 , Brenda Pardo  5   6 , Leonardo Collado-Torres  6 , Shila Ghazanfar  7 , Aaron T L Lun  8 , Stephanie C Hicks  2 , Davide Risso  1
Affiliations

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

Dario Righelli et al. Bioinformatics. .

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.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Overview of the SpatialExperiment class structure, including assays (tables of measurement values), rowData (metadata describing features), reducedDims (reduced dimension representations), colData (non-spatial and spatial metadata describing observations), spatialCoords (spatial coordinates associated with the observations) and imgData (image files and information)
See this image and copyright information in PMC

References

    1. 10x Genomics. (2020) Space Ranger: Spatial Gene Expression. https://support.10xgenomics.com/spatial-gene-expression/software/pipelin... (2 May 2022, date last accessed).
    1. 10x Genomics. (2021a) 10x Genomics Visium Spatial Gene Expression Solution (Website). https://www.10xgenomics.com/products/spatial-gene-expression (2 May 2022, date last accessed).
    1. 10x Genomics. (2021b) Mouse Brain Section Coronal (Website). https://www.10xgenomics.com/resources/datasets/mouse-brain-section-coron... (2 May 2022, date last accessed).
    1. 10x Genomics. (2021c) Spatial Gene Expression Datasets. https://support.10xgenomics.com/spatial-Gene-Expression/datasets (2 May ....
    1. Amezquita R.A. et al. (2020) Orchestrating single-cell analysis with Bioconductor. Nat. Methods, 17, 137–145. - PMC - PubMed

Publication types