SummarizedExperiment

DOI: 10.18129/B9.bioc.SummarizedExperiment    

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

SummarizedExperiment container

Bioconductor version: Development (3.15)

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, Valerie Obenchain, Jim Hester, Hervé Pagès

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Installation

To install this package, start R (version "4.2") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software
Version	1.25.3
In Bioconductor since	BioC 3.2 (R-3.2) (6.5 years)
License	Artistic-2.0
Depends	R (>= 4.0.0), methods, MatrixGenerics(>= 1.1.3), GenomicRanges(>= 1.41.5), Biobase
Imports	utils, stats, tools, Matrix, BiocGenerics(>= 0.37.0), S4Vectors(>= 0.33.7), IRanges(>= 2.23.9), GenomeInfoDb(>= 1.13.1), DelayedArray(>= 0.15.10)
LinkingTo
Suggests	HDF5Array(>= 1.7.5), annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, jsonlite, rhdf5, airway(>= 1.15.1), BiocStyle, knitr, rmarkdown, RUnit, testthat, digest
SystemRequirements
Enhances
URL	https://bioconductor.org/packages/SummarizedExperiment
BugReports	https://github.com/Bioconductor/SummarizedExperiment/issues
Depends On Me	AffiXcan, airway, AllelicImbalance, ASpediaFI, atena, bambu, BDMMAcorrect, benchmarkfdrData2019, BiocSklearn, BioPlex, BiSeq, bnbc, bodymapRat, BrainSABER, bsseq, CAGEfightR, celaref, celldex, clusterExperiment, compartmap, CoreGx, coseq, csaw, CSSQ, ctgGEM, curatedAdipoChIP, curatedAdipoRNA, curatedMetagenomicData, DaMiRseq, deco, deepSNV, DeMixT, DESeq2, DEXSeq, DiffBind, diffcoexp, diffHic, divergence, DMCFB, DMCHMM, DMRcate, DREAM4, ENmix, EnrichmentBrowser, epigenomix, evaluomeR, EventPointer, exomePeak2, ExperimentSubset, ExpressionAtlas, FEAST, fission, FlowSorted.Blood.EPIC, FRASER, GenoGAM, GenomicAlignments, GenomicFiles, GenomicSuperSignature, GRmetrics, GSEABenchmarkeR, HDCytoData, HelloRanges, hermes, HighlyReplicatedRNASeq, hipathia, HMP16SData, IgGeneUsage, InTAD, InteractionSet, IntEREst, iSEE, isomiRs, ivygapSE, lefser, lipidr, LoomExperiment, made4, MatrixQCvis, MBASED, MetaGxOvarian, MetaGxPancreas, methrix, methylPipe, MethylSeqData, MetNet, mia, miaSim, miaViz, microbiomeDataSets, microRNAome, minfi, miRmine, moanin, MouseGastrulationData, MouseThymusAgeing, mpra, MultiAssayExperiment, NADfinder, NBAMSeq, NewWave, ObMiTi, OUTRIDER, padma, pairkat, parathyroidSE, PDATK, PhIPData, profileplyr, recount, recount3, RegEnrich, REMP, restfulSE, restfulSEData, ROCpAI, rqt, runibic, sampleClassifierData, Scale4C, scAnnotatR, scGPS, scone, scTreeViz, SDAMS, SeqGate, SGSeq, signatureSearch, SingleCellExperiment, singleCellTK, SingleR, soGGi, spatialDmelxsim, spqn, spqnData, sRACIPE, ssPATHS, stageR, SummarizedBenchmark, survtype, tidySummarizedExperiment, timecoursedata, TimeSeriesExperiment, TissueEnrich, TNBC.CMS, tuberculosis, UMI4Cats, VanillaICE, VariantAnnotation, VariantExperiment, velociraptor, weitrix, yamss, zinbwave
Imports Me	ADAM, ADImpute, aggregateBioVar, airpart, ALDEx2, alpine, AlpsNMR, animalcules, anota2seq, APAlyzer, apeglm, appreci8R, ASICS, AUCell, autonomics, awst, barcodetrackR, BASiCS, batchelor, BayesSpace, bayNorm, BBCAnalyzer, benchdamic, bigPint, BiocOncoTK, BioNERO, biotmle, biovizBase, biscuiteer, BiSeq, blacksheepr, BloodCancerMultiOmics2017, BloodGen3Module, brgedata, BRGenomics, BUMHMM, BUScorrect, BUSseq, CAEN, CAGEr, CATALYST, cBioPortalData, ccfindR, celda, CelliD, CellMixS, CellTrails, censcyt, Cepo, CeTF, CHETAH, ChIPpeakAnno, ChromSCape, chromVAR, CiteFuse, CLLmethylation, clustifyr, cmapR, CNVfilteR, CNVRanger, coexnet, CoGAPS, comapr, combi, conclus, condiments, consensusDE, CopyNumberPlots, corral, COSMIC.67, countsimQC, crossmeta, curatedTCGAData, cydar, CyTOFpower, cytoKernel, cytomapper, DAMEfinder, dasper, debCAM, debrowser, DEComplexDisease, decompTumor2Sig, decoupleR, DEFormats, DEGreport, deltaCaptureC, DEP, DEScan2, DEWSeq, diffcyt, diffUTR, Dino, DiscoRhythm, distinct, dittoSeq, DominoEffect, doppelgangR, doseR, DropletUtils, Dune, easierData, easyRNASeq, eisaR, ELMER, emtdata, ensemblVEP, epialleleR, epigraHMM, epistack, epivizrData, erma, EWCE, ExpHunterSuite, FCBF, fcScan, FieldEffectCrc, FindIT2, fishpond, FLAMES, FlowSorted.CordBloodCombined.450k, fluentGenomics, GARS, gCrisprTools, GeneTonic, GenomicDataCommons, genomicInstability, getDEE2, ggbio, ggspavis, Glimma, glmGamPoi, glmSparseNet, GNET2, GreyListChIP, gscreend, GSE13015, GSVA, gwasurvivr, GWENA, HMP2Data, HTSeqGenie, HumanTranscriptomeCompendium, hummingbird, iasva, icetea, ideal, IHWpaper, ILoReg, imcRtools, infercnv, INSPEcT, InterMineR, iSEEu, iteremoval, LACE, LineagePulse, lionessR, MADSEQ, MAI, marr, MAST, mbkmeans, MBQN, mCSEA, MEAL, MEAT, MEB, metabolomicsWorkbenchR, MetaGxBreast, MetaNeighbor, metaseqR2, MethReg, MethylAid, methylscaper, methylumi, MicrobiotaProcess, midasHLA, miloR, MinimumDistance, miRLAB, miRSM, missMethyl, MLSeq, monaLisa, MoonlightR, motifbreakR, motifmatchr, MPRAnalyze, MsFeatures, msgbsR, MSPrep, msqrob2, MultiDataSet, multiOmicsViz, mumosa, muscat, musicatk, MWASTools, NanoMethViz, Nebulosa, netSmooth, NoRCE, NormalyzerDE, NxtIRFcore, oligoClasses, omicRexposome, OmicsLonDA, omicsPrint, oncomix, ORFik, OVESEG, PAIRADISE, pcaExplorer, peco, PharmacoGx, phemd, phenopath, PhosR, pipeComp, pmp, POMA, POWSC, proActiv, proDA, psichomics, pulsedSilac, PureCN, QFeatures, qsmooth, quantiseqr, R453Plus1Toolbox, RadioGx, RaggedExperiment, RareVariantVis, RcisTarget, receptLoss, regionReport, regsplice, rgsepd, Rmmquant, RNAAgeCalc, RNAsense, RnaSeqSampleSize, roar, rScudo, RTCGAToolbox, RTN, satuRn, SBGNview, SC3, SCArray, scater, scBFA, scCB2, scDblFinder, scDD, scds, scHOT, scmap, scMerge, scmeth, SCnorm, scoreInvHap, scp, scPipe, scran, scReClassify, scRepertoire, scRNAseq, scruff, scry, scTensor, scTGIF, scuttle, sechm, segmenter, seqCAT, sesame, SEtools, sigFeature, SigsPack, SingleCellMultiModal, singscore, SingscoreAMLMutations, slalom, slingshot, snapcount, SNPhood, Spaniel, SpatialCPie, spatialDE, SpatialExperiment, spatialHeatmap, spatialLIBD, spatzie, splatter, SplicingFactory, srnadiff, struct, StructuralVariantAnnotation, supersigs, switchde, systemPipeR, systemPipeTools, TabulaMurisSenisData, TBSignatureProfiler, TCGAbiolinks, TCGAbiolinksGUI, TCGAutils, TCGAWorkflow, TCGAWorkflowData, TCseq, tenXplore, tidybulk, tidySingleCellExperiment, TOAST, tomoda, ToxicoGx, tradeSeq, TrajectoryUtils, transformGamPoi, TraRe, traviz, TreeSummarizedExperiment, Trendy, tricycle, TSCAN, tscR, TSRchitect, TTMap, TVTB, tximeta, VAExprs, VariantFiltering, vidger, wpm, xcms, zellkonverter, zFPKM
Suggests Me	AnnotationHub, biobroom, BiocPkgTools, biotmleData, cageminer, CAGEWorkflow, curatedAdipoArray, curatedTBData, dcanr, dce, dearseq, DelayedArray, dorothea, DuoClustering2018, easier, edgeR, EnMCB, epivizr, epivizrChart, esetVis, fobitools, GENIE3, GenomicRanges, globalSeq, GSE103322, gsean, hca, HDF5Array, HPiP, Informeasure, InteractiveComplexHeatmap, interactiveDisplay, MatrixGenerics, MOFA2, MSnbase, ODER, pathwayPCA, philr, podkat, pRolocdata, PubScore, RforProteomics, RiboProfiling, S4Vectors, SBGNview.data, scFeatureFilter, semisup, sparrow, svaNUMT, svaRetro, systemPipeShiny, TFutils, tissueTreg
Links To Me
Build Report

Package Archives

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

Source Package	SummarizedExperiment_1.25.3.tar.gz
Windows Binary
macOS 10.13 (High Sierra)	SummarizedExperiment_1.25.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SummarizedExperiment
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SummarizedExperiment
Package Short Url	https://bioconductor.org/packages/SummarizedExperiment/
Package Downloads Report	Download Stats