SpatialExperiment

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

S4 Class for Spatially Resolved -omics Data

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DOI: 10.18129/B9.bioc.SpatialExperiment

Bioconductor version: Release (3.22)

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

Maintainer: Dario Righelli <dario.righelli at gmail.com>

Citation (from within R, enter citation("SpatialExperiment")):

Installation

To install this package, start R (version "4.5") 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 1.20.0

In Bioconductor since BioC 3.12 (R-4.0) (5 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, imcRtools, SpaceTrooper, SPIAT, tidySpatialExperiment, visiumStitched, imcdatasets, MerfishData, MouseGastrulationData, spatialLIBD, STexampleData, TENxVisiumData, VectraPolarisData, WeberDivechaLCdata

Imports Me Banksy, BulkSignalR, CARDspa, CatsCradle, concordexR, CTSV, cytomapper, DESpace, escheR, FLAMES, ggspavis, GSVA, hoodscanR, lisaClust, MoleculeExperiment, nnSVG, poem, scider, SEraster, signifinder, smoothclust, sosta, spacexr, SpaNorm, spARI, spaSim, spatialDE, SpatialExperimentIO, spatialFDA, SpatialFeatureExperiment, spatialSimGP, spicyR, spoon, SpotClean, SpotSweeper, standR, Statial, stJoincount, stPipe, SVP, tpSVG, VisiumIO, Voyager, XeniumIO, xenLite, HCATonsilData, SingleCellMultiModal, SubcellularSpatialData, TENxXeniumData, OSTA, SpatialDDLS

Suggests Me GeomxTools, ggsc, SPOTlight, zellkonverter, muSpaData

Links To Me

Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SpatialExperiment_1.20.0.tar.gz

Windows Binary (x86_64) SpatialExperiment_1.19.1.zip

macOS Binary (x86_64) SpatialExperiment_1.20.0.tgz

macOS Binary (arm64) SpatialExperiment_1.20.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/SpatialExperiment

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SpatialExperiment

Bioc Package Browser https://code.bioconductor.org/browse/SpatialExperiment/

Package Short Url https://bioconductor.org/packages/SpatialExperiment/

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