SpatialExperiment

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SpatialExperiment")

Details

Maintainer	Dario Righelli <dario.righelli@gmail.com>
Author	Dario Righelli [aut, cre] (ORCID: <https://orcid.org/0000-0003-1504-3583>), Davide Risso [aut] (ORCID: <https://orcid.org/0000-0001-8508-5012>), Helena L. Crowell [aut] (ORCID: <https://orcid.org/0000-0002-4801-1767>), Lukas M. Weber [aut] (ORCID: <https://orcid.org/0000-0002-3282-1730>), Nicholas J. Eagles [ctb]
License	GPL-3
URL	https://github.com/drighelli/SpatialExperiment
Bug Reports	https://github.com/drighelli/SpatialExperiment/issues
Downloads rank	9120
Source branch	RELEASE_3_23
biocViews	DataImport, DataRepresentation, GeneExpression, ImmunoOncology, Infrastructure, SingleCell, Software, Spatial, Transcriptomics

Documentation

Introduction to the SpatialExperiment class

Download

Source package

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 (7): Battlefield, GeomxTools, ggsc, muSpaData, SPOTlight, SVG, zellkonverter