This package is for version 3.16 of Bioconductor;
for the stable, up-to-date release version, see
SummarizedExperiment.
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]
To view documentation for the version of this package installed
in your system, start R and enter:
| biocViews |
Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software |
| Version |
1.28.0 |
| In Bioconductor since |
BioC 3.2 (R-3.2) (7.5 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 |
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| 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 |
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| Enhances |
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| 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, ENmix, EnrichmentBrowser, epigenomix, evaluomeR, EventPointer, exomePeak2, ExperimentSubset, ExpressionAtlas, extraChIPs, FEAST, fission, FRASER, GenomicAlignments, GenomicFiles, GenomicSuperSignature, GRmetrics, GSEABenchmarkeR, HDCytoData, HelloRanges, hermes, HiCDOC, HighlyReplicatedRNASeq, hipathia, HMP16SData, InTAD, InteractionSet, IntEREst, iSEE, iSEEhex, iSEEhub, ISLET, isomiRs, ivygapSE, lefser, lipidr, LoomExperiment, Macarron, made4, MatrixQCvis, MBASED, MetaGxOvarian, MetaGxPancreas, methrix, methylPipe, MethylSeqData, MetNet, mia, miaSim, miaViz, MicrobiomeBenchmarkData, microbiomeDataSets, microRNAome, minfi, miRmine, moanin, MouseGastrulationData, MouseThymusAgeing, mpra, MultiAssayExperiment, NADfinder, NBAMSeq, NewWave, ObMiTi, OUTRIDER, padma, parathyroidSE, PDATK, phenomis, PhIPData, profileplyr, qmtools, qsvaR, recount, recount3, RegEnrich, REMP, restfulSE, restfulSEData, ROCpAI, rqt, runibic, sampleClassifierData, Scale4C, scAnnotatR, scGPS, scone, scTreeViz, SDAMS, SeqGate, SEtools, SGSeq, signatureSearch, SingleCellExperiment, singleCellTK, SingleR, soGGi, spatialDmelxsim, spqn, spqnData, sRACIPE, ssPATHS, stageR, SummarizedBenchmark, survtype, TENxIO, tidySummarizedExperiment, timecoursedata, TimeSeriesExperiment, TissueEnrich, TNBC.CMS, TREG, tuberculosis, UMI4Cats, VanillaICE, VariantAnnotation, VariantExperiment, velociraptor, weitrix, yamss, zinbwave |
| Imports Me |
ADAM, ADImpute, aggregateBioVar, airpart, ALDEx2, alpine, ANCOMBC, animalcules, anota2seq, APAlyzer, apeglm, APL, appreci8R, ASICS, ASURAT, ATACseqTFEA, AUCell, autonomics, awst, barcodetrackR, BASiCS, BASiCStan, batchelor, BayesSpace, bayNorm, BBCAnalyzer, beer, benchdamic, bigPint, BiocOncoTK, BioNERO, biosigner, biotmle, biovizBase, biscuiteer, BiSeq, blacksheepr, BloodCancerMultiOmics2017, BloodGen3Module, brgedata, BRGenomics, BUMHMM, BUScorrect, BUSseq, CAEN, CAGEr, CATALYST, CBEA, 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, consICA, CopyNumberPlots, corral, COSMIC.67, countsimQC, CTSV, curatedTCGAData, cydar, CyTOFpower, cytoKernel, cytomapper, DAMEfinder, dasper, debCAM, debrowser, DEComplexDisease, decompTumor2Sig, DEFormats, DEGreport, deltaCaptureC, DEP, DEScan2, destiny, DEWSeq, diffcyt, DifferentialRegulation, diffUTR, Dino, DiscoRhythm, distinct, dittoSeq, DMRcate, DominoEffect, doppelgangR, doseR, DropletUtils, Dune, easierData, easyRNASeq, eisaR, ELMER, emtdata, ensemblVEP, epialleleR, epigraHMM, EpiMix, epimutacions, epistack, epivizrData, erma, escape, EWCE, ExpHunterSuite, FCBF, fcScan, FieldEffectCrc, FindIT2, fishpond, FLAMES, FlowSorted.Blood.EPIC, FlowSorted.CordBloodCombined.450k, fluentGenomics, FuseSOM, GARS, gCrisprTools, gemma.R, GeneTonic, genomicInstability, getDEE2, ggbio, ggspavis, Glimma, glmGamPoi, glmSparseNet, GNET2, GRaNIE, GreyListChIP, gscreend, GSE13015, GSVA, gwasurvivr, GWENA, HMP2Data, HTSeqGenie, HumanTranscriptomeCompendium, hummingbird, iasva, icetea, ideal, IgGeneUsage, IHWpaper, ILoReg, imcRtools, infercnv, INSPEcT, InterMineR, iSEEu, iteremoval, LACE, LineagePulse, lineagespot, lionessR, lisaClust, MADSEQ, MAI, marr, MAST, mbkmeans, MBQN, mCSEA, MEAL, MEAT, MEB, MerfishData, MetaboAnnotation, metabolomicsWorkbenchR, MetaGxBreast, MetaNeighbor, metaseqR2, MethReg, MethylAid, methylscaper, methylumi, MicrobiotaProcess, midasHLA, miloR, MinimumDistance, miRLAB, miRSM, missMethyl, MLInterfaces, MLSeq, monaLisa, MoonlightR, motifbreakR, motifmatchr, MPRAnalyze, MsExperiment, MsFeatures, msgbsR, MSPrep, msqrob2, MuData, MultiDataSet, multiOmicsViz, mumosa, muscat, musicatk, MWASTools, NanoMethViz, Nebulosa, NetActivity, netSmooth, nnSVG, NoRCE, NormalyzerDE, NxtIRFcore, oligoClasses, omicRexposome, OmicsLonDA, omicsPrint, omicsViewer, oncomix, ontoProc, ORFik, OVESEG, PAIRADISE, pairkat, 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, rifi, Rmmquant, RNAAgeCalc, RNAsense, RnaSeqSampleSize, roar, RolDE, ropls, rScudo, RTCGAToolbox, RTN, satuRn, SBGNview, SC3, SCArray, scater, scBFA, scCB2, scDblFinder, scDD, scDDboost, scds, scHOT, scmap, scMerge, scMET, scmeth, SCnorm, scoreInvHap, scp, scPipe, scran, scReClassify, scRepertoire, scRNAseq, scruff, scry, scTensor, scTGIF, scuttle, sechm, segmenter, seqCAT, sesame, sigFeature, signifinder, SigsPack, SimBu, simpleSeg, SingleCellMultiModal, singscore, SingscoreAMLMutations, slalom, slingshot, snapcount, SNPhood, Spaniel, spaSim, SpatialCPie, spatialDE, SpatialExperiment, SpatialFeatureExperiment, spatialHeatmap, spatialLIBD, spatzie, SPIAT, spicyR, splatter, SpliceWiz, SplicingFactory, SpotClean, srnadiff, sSNAPPY, standR, stJoincount, struct, StructuralVariantAnnotation, supersigs, switchde, systemPipeR, systemPipeTools, TabulaMurisSenisData, TBSignatureProfiler, TCGAbiolinks, TCGAbiolinksGUI, TCGAutils, TCGAWorkflow, TCGAWorkflowData, TCseq, TEKRABber, tenXplore, tidybulk, tidySingleCellExperiment, TOAST, tomoda, ToxicoGx, tradeSeq, TrajectoryUtils, transformGamPoi, TraRe, traviz, TreeSummarizedExperiment, Trendy, tricycle, TSCAN, tscR, TTMap, TVTB, tximeta, UCell, VAExprs, VariantFiltering, VDJdive, vidger, Voyager, wpm, xcms, zellkonverter, zFPKM |
| Suggests Me |
AlpsNMR, AnnotationHub, biobroom, BiocPkgTools, biotmleData, cageminer, CAGEWorkflow, curatedAdipoArray, curatedTBData, dcanr, dce, dearseq, decoupleR, 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, PSMatch, RforProteomics, RiboProfiling, S4Vectors, SBGNview.data, scFeatureFilter, semisup, sparrow, SPOTlight, svaNUMT, svaRetro, systemPipeShiny, TFutils, tissueTreg, updateObject |
| Links To Me |
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| Build Report |
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