SpatialExperiment
This is the released version of SpatialExperiment; for the devel version, see SpatialExperiment.
All Bioconductor versions of SpatialExperiment
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12
S4 Class for Spatially Resolved -omics Data
Bioconductor version: 3.23 · Package version: 1.22.0
Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordinates, images, and image metadata. A specialized constructor function is included for data from the 10x Genomics Visium platform.
Author: Dario Righelli [aut, cre] 
, Davide Risso [aut] , Helena L. Crowell [aut] , Lukas M. Weber [aut] , Nicholas J. Eagles [ctb]
Maintainer: Dario Righelli <dario.righelli at gmail.com>
Citation
From within R, enter citation("SpatialExperiment"):
Dario Righelli, Davide Risso, Helena L. Crowell, Lukas M. Weber. SpatialExperiment: S4 Class for Spatially Resolved -omics Data. doi:10.18129/B9.bioc.SpatialExperiment, R package version 1.22.0, https://bioconductor.org/packages/SpatialExperiment.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SpatialExperiment")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.22.0 |
| License | GPL-3 |
| URL | https://github.com/drighelli/SpatialExperiment |
| Bug Reports | https://github.com/drighelli/SpatialExperiment/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.12 (R-4.0) (5 years) |
| Downloads rank | 78 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, DataRepresentation, GeneExpression, ImmunoOncology, Infrastructure, SingleCell, Software, Spatial, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/SpatialExperiment/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SpatialExperiment")| Introduction to the SpatialExperiment class | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | SpatialExperiment_1.22.0.tar.gz |
| Windows binary (x86_64) | SpatialExperiment_1.22.0.zip |
| macOS binary (arm64) | SpatialExperiment_1.22.0.tgz |
| macOS binary (x86_64) | SpatialExperiment_1.22.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SpatialExperiment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SpatialExperiment |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.1.0), methods, SingleCellExperiment
Imports: rjson, grDevices, magick, utils, S4Vectors, SummarizedExperiment, BiocGenerics, BiocFileCache
Suggests: knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils, VisiumIO
Reverse dependencies
Depends On Me (17): alabaster.spatial, clustSIGNAL, ExperimentSubset, imcdatasets, imcRtools, MerfishData, MouseGastrulationData, SpaceTrooper, SpatialDatasets, spatialLIBD, SPIAT, STexampleData, TENxVisiumData, tidySpatialExperiment, VectraPolarisData, visiumStitched, WeberDivechaLCdata
Imports Me (60): Banksy, blisa, BulkSignalR, CARDspa, CatsCradle, concordexR, CTSV, cytomapper, DenoIST, DESpace, escheR, FLAMES, ggspavis, GSVA, GSVAdata, HCATonsilData, HistoImagePlot, hoodscanR, humanHippocampus2024, imageFeatureTCGA, imageTCGAutils, jazzPanda, lisaClust, MoleculeExperiment, nnSVG, poem, scider, SEraster, signifinder, SingleCellMultiModal, smoothclust, smoppix, sosta, spacexr, SpaNorm, spARI, spaSim, SpatialArtifacts, spatialDE, SpatialExperimentIO, spatialFDA, SpatialFeatureExperiment, spatialSimGP, spicyR, SpNeigh, spoon, SpotClean, SpotSweeper, standR, Statial, stJoincount, stPipe, SubcellularSpatialData, SVP, TENxXeniumData, tpSVG, VisiumIO, Voyager, XeniumIO, xenLite
Suggests Me (8): Battlefield, GeomxTools, ggsc, muSpaData, RGraphSpace, SPOTlight, SVG, zellkonverter