SpatialExperiment

This is thereleased version of SpatialExperiment; for the devel version, seeSpatialExperiment.

S4 Class for Spatially Resolved -omics Data

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: 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, entercitation("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 appropriateBioconductor 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
Suggests Me	GeomxTools,ggsc,SPOTlight,zellkonverter,muSpaData
Links To Me
Build Report	Build Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source Package	SpatialExperiment_1.20.0.tar.gz
Windows Binary (x86_64)	SpatialExperiment_1.20.0.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/
Package Downloads Report	Download Stats

Movatterモバイル変換

Menu