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SummarizedExperiment

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

SummarizedExperiment container


Bioconductor version: Development (3.20)

The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.

Author: Martin Morgan [aut], Valerie Obenchain [aut], Jim Hester [aut], Hervé Pagès [aut, cre]

Maintainer: Hervé Pagès <hpages.on.github at gmail.com>

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

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("SummarizedExperiment")

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("SummarizedExperiment")
1. SummarizedExperiment for Coordinating Experimental Assays, Samples, and Regions of Interest HTML R Script
2. Extending the SummarizedExperiment class HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software
Version 1.35.1
In Bioconductor since BioC 3.2 (R-3.2) (9 years)
License Artistic-2.0
Depends R (>= 4.0.0), methods, MatrixGenerics(>= 1.1.3), GenomicRanges(>= 1.55.2), Biobase
Imports utils, stats, tools, Matrix, BiocGenerics(>= 0.37.0), S4Vectors(>= 0.33.7), IRanges(>= 2.23.9), GenomeInfoDb(>= 1.13.1), S4Arrays(>= 1.1.1), DelayedArray(>= 0.27.1)
System Requirements
URL https://bioconductor.org/packages/SummarizedExperiment
Bug Reports https://github.com/Bioconductor/SummarizedExperiment/issues
See More
Suggests jsonlite, rhdf5, HDF5Array(>= 1.7.5), annotate, AnnotationDbi, GenomicFeatures, SparseArray, SingleCellExperiment, TxDb.Hsapiens.UCSC.hg19.knownGene, hgu95av2.db, airway(>= 1.15.1), BiocStyle, knitr, rmarkdown, RUnit, testthat, digest
Linking To
Enhances
Depends On Me AffiXcan, alabaster.se, AllelicImbalance, atena, bambu, betaHMM, BiocSklearn, BiSeq, bnbc, broadSeq, bsseq, CAGEfightR, celaref, clusterExperiment, CoreGx, coseq, csaw, CSSQ, DaMiRseq, deepSNV, DeMixT, DESeq2, DEXSeq, DiffBind, diffcoexp, diffHic, dinoR, divergence, DMCFB, DMCHMM, EnrichmentBrowser, epigenomix, evaluomeR, EventPointer, ExperimentSubset, ExpressionAtlas, extraChIPs, FEAST, FRASER, GenomicAlignments, GenomicFiles, GenomicSuperSignature, GRmetrics, GSEABenchmarkeR, HelloRanges, hermes, HERON, HiCDOC, hipathia, InteractionSet, IntEREst, iSEE, iSEEhex, iSEEhub, iSEEindex, ISLET, isomiRs, ivygapSE, lefser, lipidr, LoomExperiment, lute, Macarron, made4, MatrixQCvis, MBASED, methodical, methrix, methylPipe, MetNet, MGnifyR, mia, miaViz, MICSQTL, minfi, moanin, mpra, MultiAssayExperiment, multistateQTL, NADfinder, NBAMSeq, NewWave, orthos, OUTRIDER, padma, PDATK, phenomis, PhIPData, profileplyr, qmtools, qsvaR, QTLExperiment, recount, recount3, RegEnrich, REMP, ROCpAI, runibic, Scale4C, scAnnotatR, scGPS, scone, screenCounter, scTreeViz, SDAMS, sechm, SeqGate, SEtools, SGSeq, signatureSearch, SingleCellExperiment, singleCellTK, SingleR, soGGi, spillR, spqn, ssPATHS, stageR, survtype, TENxIO, tidyCoverage, tidySummarizedExperiment, TissueEnrich, TREG, UMI4Cats, VanillaICE, VariantAnnotation, VariantExperiment, velociraptor, weitrix, yamss, zinbwave, airway, benchmarkfdrData2019, BioPlex, bodymapRat, celldex, curatedAdipoChIP, curatedAdipoRNA, curatedMetagenomicData, fission, HDCytoData, HighlyReplicatedRNASeq, HMP16SData, MetaGxOvarian, MetaGxPancreas, MethylSeqData, MicrobiomeBenchmarkData, microbiomeDataSets, microRNAome, MouseGastrulationData, MouseThymusAgeing, ObMiTi, parathyroidSE, sampleClassifierData, scMultiome, spatialDmelxsim, spqnData, timecoursedata, tuberculosis, TumourMethData, DRomics, OncoSubtype, ordinalbayes
Imports Me ADAM, ADImpute, aggregateBioVar, airpart, ALDEx2, ANCOMBC, animalcules, anota2seq, APAlyzer, apeglm, APL, appreci8R, ASICS, ASURAT, ATACseqTFEA, AUCell, autonomics, awst, Banksy, barcodetrackR, BASiCS, BASiCStan, batchelor, BatchQC, BayesSpace, bayNorm, BBCAnalyzer, beer, benchdamic, BERT, bettr, BioGA, BioNERO, biosigner, biotmle, biovizBase, biscuiteer, BiSeq, blacksheepr, BloodGen3Module, BUMHMM, BUScorrect, BUSseq, CaDrA, CAGEr, CATALYST, CBEA, cBioPortalData, ccfindR, CDI, celda, CelliD, CellMixS, CellScore, CellTrails, censcyt, Cepo, CeTF, CHETAH, ChIPpeakAnno, ChromSCape, chromVAR, CiteFuse, clustifyr, cmapR, CNVfilteR, CNVRanger, CoGAPS, comapr, combi, condiments, consensusDE, consICA, CopyNumberPlots, corral, countsimQC, CTexploreR, CTSV, CuratedAtlasQueryR, cydar, cypress, CyTOFpower, cytofQC, cytoKernel, cytomapper, cytoviewer, DAMEfinder, debCAM, debrowser, decompTumor2Sig, decontX, DEFormats, DEGreport, DELocal, deltaCaptureC, demuxSNP, DEP, DEScan2, DESpace, destiny, DEWSeq, diffcyt, DifferentialRegulation, diffUTR, Dino, DiscoRhythm, distinct, dittoSeq, DMRcate, DominoEffect, doppelgangR, doseR, dreamlet, DropletUtils, Dune, eisaR, ELMER, epialleleR, epigraHMM, EpiMix, epimutacions, epiregulon, epiregulon.extra, epistack, epivizrData, erma, escape, escheR, EWCE, fcScan, FeatSeekR, findIPs, FindIT2, fishpond, FLAMES, FuseSOM, GARS, gCrisprTools, gDNAx, gDRcore, gDRimport, gDRutils, gemma.R, GeneTonic, genomicInstability, GeoTcgaData, getDEE2, ggbio, ggsc, ggspavis, Glimma, glmGamPoi, glmSparseNet, GRaNIE, GreyListChIP, gscreend, GSVA, gwasurvivr, GWENA, HarmonizR, HiContacts, hoodscanR, HTSeqGenie, hummingbird, HybridExpress, iasva, icetea, ideal, IFAA, IgGeneUsage, ILoReg, imcRtools, iNETgrate, infercnv, INSPEcT, iSEEde, iSEEfier, iSEEpathways, iSEEu, IsoBayes, IsoformSwitchAnalyzeR, LACE, lemur, limpca, lineagespot, lionessR, lisaClust, MADSEQ, MAI, mariner, marr, MAST, mastR, mbkmeans, MBQN, mCSEA, MEAL, MEAT, MEB, MetaboAnnotation, metabolomicsWorkbenchR, MetaNeighbor, metaseqR2, MethReg, MethylAid, methyLImp2, methylscaper, methylumi, miaSim, MicrobiotaProcess, midasHLA, miloR, MinimumDistance, miRSM, missMethyl, MLInterfaces, MLSeq, mobileRNA, monaLisa, MoonlightR, mosdef, motifbreakR, motifmatchr, MPAC, MPRAnalyze, MsExperiment, MsFeatures, MSPrep, msqrob2, MuData, MultiDataSet, MultiRNAflow, multiWGCNA, mumosa, muscat, musicatk, MWASTools, NanoMethViz, Nebulosa, NetActivity, netSmooth, nipalsMCIA, nnSVG, NormalyzerDE, oligoClasses, omicRexposome, omicsPrint, omicsViewer, oncomix, ORFik, OVESEG, PAIRADISE, pairedGSEA, pairkat, pcaExplorer, peco, PepSetTest, pgxRpi, PharmacoGx, phenopath, PhosR, pipeComp, Pirat, PIUMA, planttfhunter, pmp, PolySTest, POMA, POWSC, proActiv, proDA, psichomics, PureCN, QFeatures, qsmooth, quantiseqr, R453Plus1Toolbox, RadioGx, raer, RaggedExperiment, RareVariantVis, RcisTarget, receptLoss, RegionalST, regionReport, regsplice, rgsepd, rifi, rifiComparative, Rmmquant, RNAAgeCalc, RNAsense, roar, RolDE, ropls, rScudo, RTCGAToolbox, RTN, saseR, satuRn, SBGNview, SC3, SCArray, SCArray.sat, scater, scBFA, scCB2, scDblFinder, scDD, scDDboost, scDesign3, scds, scHOT, scider, scmap, scMerge, scMET, scmeth, scMultiSim, SCnorm, scoreInvHap, scp, scPipe, scran, scReClassify, scRepertoire, scruff, scry, scTensor, scTGIF, scuttle, scviR, segmenter, seqCAT, sesame, SGCP, sigFeature, SigsPack, SimBu, simPIC, simpleSeg, SingleCellAlleleExperiment, singscore, slalom, slingshot, smartid, smoothclust, snapcount, SNPhood, Spaniel, spaSim, SpatialCPie, spatialDE, SpatialExperiment, SpatialFeatureExperiment, spatialHeatmap, spatzie, SPIAT, spicyR, splatter, SpliceWiz, SplicingFactory, spoon, SpotClean, SpotSweeper, srnadiff, sSNAPPY, standR, Statial, stJoincount, struct, StructuralVariantAnnotation, supersigs, SurfR, SVMDO, switchde, systemPipeR, systemPipeTools, TBSignatureProfiler, TCGAbiolinks, TCGAutils, TCseq, tidybulk, tidySingleCellExperiment, tidySpatialExperiment, TOAST, tomoda, ToxicoGx, tpSVG, tradeSeq, TrajectoryUtils, transformGamPoi, transmogR, traviz, treeclimbR, TreeSummarizedExperiment, Trendy, tricycle, TSCAN, TTMap, TVTB, tximeta, UCell, VAExprs, VariantFiltering, VDJdive, vidger, VisiumIO, Voyager, wpm, xcms, zellkonverter, zFPKM, BloodCancerMultiOmics2017, brgedata, CLLmethylation, COSMIC.67, curatedTCGAData, easierData, emtdata, FieldEffectCrc, FlowSorted.Blood.EPIC, FlowSorted.CordBloodCombined.450k, GSE13015, HCATonsilData, HiBED, HMP2Data, homosapienDEE2CellScore, IHWpaper, MerfishData, MetaGxBreast, MetaScope, orthosData, scRNAseq, SingleCellMultiModal, spatialLIBD, TabulaMurisSenisData, TCGAWorkflowData, TENxXeniumData, ExpHunterSuite, fluentGenomics, SingscoreAMLMutations, TCGAWorkflow, autoGO, digitalDLSorteR, DWLS, ggpicrust2, HeritSeq, imcExperiment, karyotapR, MetAlyzer, microbial, MOCHA, PlasmaMutationDetector, PlasmaMutationDetector2, RCPA, RNAseqQC, SC.MEB, SCIntRuler, SCRIP, scROSHI, SpatialDDLS, treediff, VSOLassoBag
Suggests Me alabaster.mae, AlpsNMR, AnnotationHub, BindingSiteFinder, biobroom, BiocPkgTools, cageminer, CTdata, dar, dcanr, dce, dearseq, decoupleR, DelayedArray, easier, edgeR, EnMCB, epivizr, epivizrChart, esetVis, fobitools, funOmics, gDR, GENIE3, GenomicRanges, globalSeq, gsean, hca, HDF5Array, HPiP, Informeasure, InteractiveComplexHeatmap, interactiveDisplay, knowYourCG, MatrixGenerics, microSTASIS, MOFA2, MSnbase, pathwayPCA, philr, podkat, PSMatch, RiboProfiling, Rvisdiff, S4Vectors, scFeatureFilter, semisup, sketchR, SPOTlight, svaNUMT, svaRetro, systemPipeShiny, TFutils, biotmleData, curatedAdipoArray, curatedTBData, dorothea, DuoClustering2018, gDRtestData, GSE103322, multiWGCNAdata, pRolocdata, RforProteomics, SBGNview.data, tissueTreg, CAGEWorkflow, Canek, clustree, conos, CytoSimplex, dyngen, file2meco, lfc, MiscMetabar, polyRAD, RaceID, rliger, seqgendiff, Seurat, Signac, singleCellHaystack, teal.slice, tidydr, volcano3D
Links To Me
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Package Archives

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

Source Package SummarizedExperiment_1.35.1.tar.gz
Windows Binary SummarizedExperiment_1.35.1.zip
macOS Binary (x86_64) SummarizedExperiment_1.35.1.tgz
macOS Binary (arm64) SummarizedExperiment_1.35.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/SummarizedExperiment
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SummarizedExperiment
Bioc Package Browser https://code.bioconductor.org/browse/SummarizedExperiment/
Package Short Url https://bioconductor.org/packages/SummarizedExperiment/
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