SummarizedExperiment

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SummarizedExperiment.

SummarizedExperiment container

Installation

To install this package, start R (version "4.0") and enter:

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

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	1.20.0
In Bioconductor since	BioC 3.2 (R-3.2) (8.5 years)
License	Artistic-2.0
Depends	R (>= 3.2), methods, MatrixGenerics(>= 1.1.3), GenomicRanges(>= 1.41.5), Biobase
Imports	utils, stats, tools, Matrix, BiocGenerics(>= 0.15.3), S4Vectors(>= 0.27.12), IRanges(>= 2.23.9), GenomeInfoDb(>= 1.13.1), DelayedArray(>= 0.15.10)
System Requirements
URL	https://bioconductor.org/packages/SummarizedExperiment
Bug Reports	https://github.com/Bioconductor/SummarizedExperiment/issues

See More

Suggests	HDF5Array(>= 1.7.5), annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, jsonlite, rhdf5, airway, BiocStyle, knitr, rmarkdown, RUnit, testthat, digest
Linking To
Enhances
Depends On Me	AffiXcan, airway, AllelicImbalance, ASpediaFI, bambu, BDMMAcorrect, benchmarkfdrData2019, BiocSklearn, BiSeq, bnbc, bodymapRat, BrainSABER, bsseq, CAGEfightR, celaref, celldex, clusterExperiment, coseq, csaw, CSSQ, ctgGEM, curatedAdipoChIP, curatedAdipoRNA, DaMiRseq, deco, deepSNV, DeMixT, DESeq2, DEXSeq, DiffBind, diffcoexp, diffHic, divergence, DMCFB, DMCHMM, DMRcate, DREAM4, dsQTL, ENmix, EnrichmentBrowser, epigenomix, evaluomeR, EventPointer, exomePeak2, ExperimentSubset, ExpressionAtlas, fission, FlowSorted.Blood.EPIC, FlowSorted.CordBloodCombined.450k, FRASER, GenoGAM, GenomicAlignments, GenomicFiles, genoset, geuvPack, GRmetrics, GSEABenchmarkeR, HDCytoData, HelloRanges, HighlyReplicatedRNASeq, hipathia, HMP16SData, IgGeneUsage, InTAD, InteractionSet, IntEREst, iSEE, isomiRs, ivygapSE, JunctionSeq, lefser, lipidr, LoomExperiment, made4, MBASED, MetaGxOvarian, MetaGxPancreas, methrix, methylPipe, MethylSeqData, microRNAome, minfi, miRmine, MouseGastrulationData, mpra, MultiAssayExperiment, NADfinder, NBAMSeq, NewWave, OUTRIDER, padma, parathyroidSE, profileplyr, recount, recount3, RegEnrich, REMP, restfulSE, restfulSEData, ROCpAI, rqt, runibic, sampleClassifierData, Scale4C, scGPS, scone, SDAMS, SeqGate, SGSeq, signatureSearch, simulatorZ, SingleCellExperiment, singleCellTK, SingleR, soGGi, Spaniel, spqn, spqnData, sRACIPE, ssPATHS, stageR, SummarizedBenchmark, survtype, tidySummarizedExperiment, timecoursedata, TimeSeriesExperiment, TissueEnrich, TNBC.CMS, UMI4Cats, VanillaICE, VariantAnnotation, VariantExperiment, velociraptor, weitrix, yamss, zinbwave
Imports Me	ADAM, adaptest, ADImpute, aggregateBioVar, ALDEx2, alpine, AlpsNMR, animalcules, anota2seq, APAlyzer, apeglm, appreci8R, ASICS, AUCell, BASiCS, batchelor, BayesSpace, bayNorm, BBCAnalyzer, bigPint, BiocOncoTK, biotmle, biovizBase, biscuiteer, BiSeq, blacksheepr, BloodCancerMultiOmics2017, brgedata, BRGenomics, BUMHMM, BUScorrect, CAGEr, CATALYST, cBioPortalData, ccfindR, celda, CellMixS, CellTrails, CeTF, CHARGE, CHETAH, ChIPpeakAnno, ChromSCape, chromVAR, CiteFuse, CLLmethylation, clustifyr, cmapR, CNVfilteR, CNVRanger, coexnet, CoGAPS, combi, compartmap, consensusDE, CopyNumberPlots, CoreGx, corral, COSMIC.67, countsimQC, curatedTCGAData, cydar, cytomapper, DAMEfinder, dasper, debCAM, debrowser, DEComplexDisease, decompTumor2Sig, DEFormats, DEGreport, deltaCaptureC, DEP, DEScan2, destiny, DEWSeq, diffcyt, DiscoRhythm, distinct, dittoSeq, DominoEffect, doppelgangR, doseR, DropletUtils, Dune, easyRNASeq, eisaR, ELMER, ensemblVEP, epivizrData, erma, FCBF, fcScan, FieldEffectCrc, fishpond, fluentGenomics, FourCSeq, GARS, gCrisprTools, GeneTonic, GenomicDataCommons, getDEE2, GGBase, ggbio, Glimma, glmGamPoi, glmSparseNet, GNET2, gQTLBase, gQTLstats, gramm4R, GreyListChIP, gscreend, GSVA, gwasurvivr, GWENA, HMP2Data, HTSeqGenie, HumanTranscriptomeCompendium, hummingbird, iasva, icetea, ideal, IHWpaper, ILoReg, ImpulseDE2, infercnv, INSPEcT, InterMineR, iSEEu, iteremoval, LACE, LineagePulse, lionessR, MADSEQ, marr, MAST, mbkmeans, MBQN, mCSEA, MEAL, MEAT, MEB, metabolomicsWorkbenchR, MetaGxBreast, MetaNeighbor, metaseqR2, MethReg, methyAnalysis, MethylAid, methylumi, methyvim, MinimumDistance, miRLAB, miRSM, missMethyl, MLSeq, MoonlightR, motifbreakR, motifmatchr, MPRAnalyze, msgbsR, MSPrep, MultiDataSet, multiOmicsViz, muscat, musicatk, MWASTools, NanoMethViz, Nebulosa, netSmooth, NoRCE, NormalyzerDE, oligoClasses, omicRexposome, OmicsLonDA, omicsPrint, oncomix, ORFik, OVESEG, PAIRADISE, pcaExplorer, peco, PharmacoGx, phemd, phenopath, pipeComp, pmp, proActiv, proDA, psichomics, pulsedSilac, PureCN, QFeatures, qsmooth, R453Plus1Toolbox, RadioGx, RaggedExperiment, RareVariantVis, RcisTarget, receptLoss, regionReport, regsplice, rgsepd, Rmmquant, RNAAgeCalc, RNAsense, roar, rScudo, RTCGAToolbox, RTN, SBGNview, SC3, scater, scBFA, scCB2, scDblFinder, scDD, scds, scHOT, scmap, scMerge, scmeth, SCnorm, scoreInvHap, scp, scPipe, scran, scRepertoire, scRNAseq, scruff, scry, scTensor, scTGIF, scuttle, seqCAT, sesame, SEtools, sigFeature, SigsPack, SingleCellMultiModal, singscore, SingscoreAMLMutations, slalom, slingshot, slinky, snapcount, SNPhood, SpatialCPie, spatialHeatmap, spatialLIBD, splatter, srnadiff, struct, SVAPLSseq, switchde, systemPipeR, TBSignatureProfiler, TCGAbiolinks, TCGAbiolinksGUI, TCGAutils, TCGAWorkflow, TCGAWorkflowData, TCseq, tenXplore, tidybulk, TOAST, tomoda, ToPASeq, ToxicoGx, tradeSeq, TreeSummarizedExperiment, Trendy, TSCAN, tscR, TSRchitect, TTMap, TVTB, tximeta, TxRegInfra, VariantFiltering, vidger, wpm, xcms, yriMulti, zellkonverter, zFPKM
Suggests Me	AnnotationHub, biobroom, BiocPkgTools, biotmleData, CAGEWorkflow, curatedAdipoArray, dcanr, dearseq, DelayedArray, dorothea, DuoClustering2018, edgeR, EnMCB, epivizr, epivizrChart, esetVis, GENIE3, GenomicRanges, globalSeq, gsean, HDF5Array, Informeasure, interactiveDisplay, MatrixGenerics, methyvimData, MOFA2, MSnbase, pathprint, pathprintGEOData, pathwayPCA, podkat, PubScore, RforProteomics, RiboProfiling, S4Vectors, SBGNview.data, scFeatureFilter, semisup, StructuralVariantAnnotation, systemPipeShiny, TFutils, tissueTreg
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	SummarizedExperiment_1.20.0.tar.gz
Windows Binary	SummarizedExperiment_1.20.0.zip
macOS 10.13 (High Sierra)	SummarizedExperiment_1.20.0.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/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.12	Source Archive