SpatialExperiment

This is the released version of SpatialExperiment; for the devel version, see SpatialExperiment.

All versions

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: Release (3.23)

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] ORCID: 0000-0003-1504-3583 , Davide Risso [aut] ORCID: 0000-0001-8508-5012 , Helena L. Crowell [aut] ORCID: 0000-0002-4801-1767 , Lukas M. Weber [aut] ORCID: 0000-0002-3282-1730 , 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.

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	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DataRepresentation, GeneExpression, ImmunoOncology, Infrastructure, SingleCell, Software, Spatial, Transcriptomics
Version	1.22.0
In Bioconductor since	BioC 3.12 (R-4.0) (6 years)
License	GPL-3
Depends	R (>= 4.1.0), methods, SingleCellExperiment
Imports	rjson, grDevices, magick, utils, S4Vectors, SummarizedExperiment, BiocGenerics, BiocFileCache
System Requirements
URL	https://github.com/drighelli/SpatialExperiment
Bug Reports	https://github.com/drighelli/SpatialExperiment/issues

Suggests	knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils, VisiumIO
Linking To
Enhances
Depends On Me	alabaster.spatial, clustSIGNAL, ExperimentSubset, imcdatasets, imcRtools, MerfishData, MouseGastrulationData, SpaceTrooper, SpatialDatasets, spatialLIBD, SPIAT, STexampleData, TENxVisiumData, tidySpatialExperiment, VectraPolarisData, visiumStitched, WeberDivechaLCdata
Imports Me	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, OSTA, 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	Battlefield, GeomxTools, ggsc, muSpaData, RGraphSpace, SPOTlight, SVG, zellkonverter
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow 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 (big-sur-x86_64)	SpatialExperiment_1.22.0.tgz
macOS Binary (sonoma-arm64)	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 Short Url	https://bioconductor.org/packages/SpatialExperiment/
Package Downloads Report	Download Stats