SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor.
basic_science · Level V
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- Record sourced from PubMed, PMID 35482478.
- Also identified by DOI 10.1093/bioinformatics/btac299 and PMC identifier 9154247.
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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. 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 data are available at Bioinformatics online.
Medical subject headings
- Software
- Transcriptome