ArticleBioinformatics (Oxford, England)2022
SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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Who cites it
92 citing papers in PubMed.
- Characterizing intra- and intertumor heterogeneity in ovarian high-grade serous carcinoma subtypes using single-cell and spatial transcriptomics.Genome research · 2026Article
- Three dimensional reconstruction of the human nucleus accumbens reveals topographic organization and molecular heterogeneity of D1-islands across the anterior posterior axis.bioRxiv : the preprint server for biology · 2026Article
- Article
- Integrative Transcriptomic Profiling Delineates LTBP4-Driven Fibroblast Reprogramming Across the Ossification Continuum of the Ligamentum Flavum.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Article
- Molecular programs in human locus coeruleus link APOE and neuromelanin to Alzheimer's vulnerability.Acta neuropathologica · 2026Article
- scDiagnostics: systematic assessment of cell type annotation in single-cell transcriptomics data.Briefings in bioinformatics · 2026Article
- CAR19 Tregs treat murine chronic graft-versus-host disease through immune suppression without measurable B cell cytolysis.JCI insight · 2026Article
- Spatialproteomics: an interoperable toolbox for analyzing highly multiplexed fluorescence image data.Nature methods · 2026Article
- Dynamic remodeling of the pancreas immune landscape in obesity.Nature communications · 2026Article
- Reproducible-by-design: Romics Processor, a FAIR ecosystem for multi-omics and spatial-omics analysis.bioRxiv : the preprint server for biology · 2026Article
- BatchSVG: identifying batch-biased genes in the application of spatially variable gene detection.Bioinformatics (Oxford, England) · 2026Article
- Spatiomolecular mapping reveals anatomical organization of heterogeneous cell types in the human nucleus accumbens.Neuron · 2026Article
- Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain.Cell reports · 2026Article
- Review
- DeeDeeExperiment: building an infrastructure for integrating and managing omics data analysis results in R/Bioconductor.Bioinformatics (Oxford, England) · 2026Article
- Molecular profiling of sacral chordomas through methylation, spatial transcriptomics and multiplexed immunofluorescence.ESMO rare cancers · 2026Article
- InSituPy: a framework for histology-guided, multi-sample analysis of single-cell spatial omics data.Bioinformatics (Oxford, England) · 2026Article
- Spatially resolved molecular sex differences at single-cell resolution in the adult human ventromedial and arcuate hypothalamus.Cell reports · 2026Article
- An integrative spatial multi-omic workflow for unified analysis of tumor tissue.Cell reports methods · 2026Article
- Mapping spatially organized molecular and genetic signatures of schizophrenia across multiple scales in human prefrontal cortex.bioRxiv : the preprint server for biology · 2026Article
32 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
summarySpatialExperiment 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.