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Bioconductor - SpatialExperiment (development version)

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 (3.22)

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: 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")): Installation

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

Details biocViews DataImport, DataRepresentation, GeneExpression, ImmunoOncology, Infrastructure, SingleCell, Software, Spatial, Transcriptomics Version 1.19.1 In Bioconductor since BioC 3.12 (R-4.0) (4.5 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 See More Suggests knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils, VisiumIO Linking To Enhances Depends On Me alabaster.spatial, clustSIGNAL, ExperimentSubset, imcRtools, 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, spaSim, spatialDE, SpatialExperimentIO, spatialFDA, SpatialFeatureExperiment, spatialSimGP, spicyR, spoon, SpotClean, SpotSweeper, standR, Statial, stJoincount, SVP, tpSVG, VisiumIO, Voyager, XeniumIO, xenLite, HCATonsilData, SingleCellMultiModal, SubcellularSpatialData, TENxXeniumData, 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.

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