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Updated: Sep 25, 2025
Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
Published on: January 10, 2019
SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor
Dario Righelli1, Lukas M Weber2, Helena L Crowell3,4
1Department of Statistical Sciences, University of Padova, 35121 Padova, Italy.
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.
