Welcome to the new bioconductor.org!

SpatialExperiment

This is the development version of SpatialExperiment; for the stable release version, see SpatialExperiment.

S4 Class for Spatially Resolved -omics Data


Bioconductor version: Development (3.19)

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")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews DataImport, DataRepresentation, GeneExpression, ImmunoOncology, Infrastructure, SingleCell, Software, Spatial, Transcriptomics
Version 1.13.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3
Depends 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
See More
Suggests knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils
Linking To
Enhances
Depends On Me alabaster.spatial, ExperimentSubset, imcdatasets, imcRtools, MerfishData, MouseGastrulationData, SpatialDatasets, spatialLIBD, SPIAT, STexampleData, TENxVisiumData, tidySpatialExperiment, VectraPolarisData, WeberDivechaLCdata
Imports Me Banksy, CTSV, cytomapper, DESpace, escheR, ggspavis, HCATonsilData, hoodscanR, lisaClust, MoleculeExperiment, nnSVG, scFeatures, scider, signifinder, SingleCellMultiModal, spaSim, spatialDE, SpatialFeatureExperiment, spicyR, SpotClean, standR, Statial, stJoincount, SubcellularSpatialData, TENxXeniumData, VisiumIO, Voyager
Suggests Me GeomxTools, ggsc, SPOTlight
Links To Me
Build Report Build Report

Package Archives

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

Source Package SpatialExperiment_1.13.0.tar.gz
Windows Binary SpatialExperiment_1.13.0.zip
macOS Binary (x86_64) SpatialExperiment_1.13.0.tgz
macOS Binary (arm64) SpatialExperiment_1.13.0.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/
Package Downloads Report Download Stats