This package is for version 3.13 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.
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 |
1.22.0 |
| In Bioconductor since |
BioC 3.2 (R-3.2) (6 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(>= 0.27.12), 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, 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, bambu, BDMMAcorrect, benchmarkfdrData2019, BiocSklearn, 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, dsQTL, ENmix, EnrichmentBrowser, epigenomix, evaluomeR, EventPointer, exomePeak2, ExperimentSubset, ExpressionAtlas, FEAST, fission, FlowSorted.Blood.EPIC, FlowSorted.CordBloodCombined.450k, FRASER, GenoGAM, GenomicAlignments, GenomicFiles, GenomicSuperSignature, genoset, GRmetrics, GSEABenchmarkeR, HDCytoData, HelloRanges, HighlyReplicatedRNASeq, hipathia, HMP16SData, IgGeneUsage, InTAD, InteractionSet, IntEREst, iSEE, isomiRs, ivygapSE, lefser, lipidr, LoomExperiment, made4, MatrixQCvis, MBASED, MetaGxOvarian, MetaGxPancreas, methrix, methylPipe, MethylSeqData, MetNet, mia, miaViz, microbiomeDataSets, microRNAome, minfi, miRmine, moanin, MouseGastrulationData, MouseThymusAgeing, mpra, MultiAssayExperiment, NADfinder, NBAMSeq, NewWave, ObMiTi, OUTRIDER, padma, parathyroidSE, PDATK, PhIPData, profileplyr, recount, recount3, RegEnrich, REMP, restfulSE, restfulSEData, ROCpAI, rqt, runibic, sampleClassifierData, Scale4C, scClassifR, scGPS, scone, SDAMS, SeqGate, SGSeq, signatureSearch, simulatorZ, SingleCellExperiment, singleCellTK, SingleR, soGGi, spqn, spqnData, sRACIPE, ssPATHS, stageR, SummarizedBenchmark, survtype, tidySummarizedExperiment, timecoursedata, TimeSeriesExperiment, TissueEnrich, TNBC.CMS, 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, bigPint, BiocOncoTK, BioNERO, biotmle, biovizBase, biscuiteer, BiSeq, blacksheepr, BloodCancerMultiOmics2017, BloodGen3Module, brgedata, BRGenomics, BUMHMM, BUScorrect, CAEN, CAGEr, CATALYST, cBioPortalData, ccfindR, celda, CelliD, CellMixS, CellTrails, censcyt, CeTF, CHETAH, ChIPpeakAnno, ChromSCape, chromVAR, CiteFuse, CLLmethylation, clustifyr, cmapR, CNVfilteR, CNVRanger, coexnet, CoGAPS, combi, conclus, condiments, consensusDE, CopyNumberPlots, corral, COSMIC.67, countsimQC, crossmeta, curatedTCGAData, cydar, cytomapper, DAMEfinder, dasper, debCAM, debrowser, DEComplexDisease, decompTumor2Sig, DEFormats, DEGreport, deltaCaptureC, DEP, DEScan2, destiny, DEWSeq, diffcyt, diffUTR, DiscoRhythm, distinct, dittoSeq, DominoEffect, doppelgangR, doseR, DropletUtils, Dune, easyRNASeq, eisaR, ELMER, emtdata, ensemblVEP, epialleleR, epigraHMM, epivizrData, erma, EWCE, ExpHunterSuite, FCBF, fcScan, FieldEffectCrc, fishpond, fluentGenomics, GARS, gCrisprTools, GeneTonic, GenomicDataCommons, getDEE2, ggbio, Glimma, glmGamPoi, glmSparseNet, GNET2, gramm4R, GreyListChIP, gscreend, GSE13015, GSVA, gwasurvivr, GWENA, HMP2Data, HTSeqGenie, HumanTranscriptomeCompendium, hummingbird, iasva, icetea, ideal, IHWpaper, ILoReg, infercnv, INSPEcT, InterMineR, iSEEu, iteremoval, LACE, LineagePulse, lionessR, MADSEQ, marr, MAST, mbkmeans, MBQN, mCSEA, MEAL, MEAT, MEB, metabolomicsWorkbenchR, MetaGxBreast, MetaNeighbor, metaseqR2, MethReg, methyAnalysis, MethylAid, methylscaper, methylumi, MicrobiotaProcess, midasHLA, miloR, MinimumDistance, miRLAB, miRSM, missMethyl, MLSeq, MoonlightR, motifbreakR, motifmatchr, MPRAnalyze, MsFeatures, msgbsR, MSPrep, msqrob2, MultiDataSet, multiOmicsViz, mumosa, muscat, musicatk, MWASTools, NanoMethViz, Nebulosa, netSmooth, NoRCE, NormalyzerDE, oligoClasses, omicRexposome, OmicsLonDA, omicsPrint, oncomix, ORFik, OVESEG, PAIRADISE, pcaExplorer, peco, PharmacoGx, phemd, phenopath, PhosR, pipeComp, pmp, POWSC, proActiv, proDA, psichomics, pulsedSilac, PureCN, QFeatures, qsmooth, quantiseqr, R453Plus1Toolbox, RadioGx, RaggedExperiment, RareVariantVis, RcisTarget, receptLoss, regionReport, regsplice, rgsepd, Rmmquant, RNAAgeCalc, RNAsense, roar, rScudo, RTCGAToolbox, RTN, satuRn, SBGNview, SC3, SCArray, scater, scBFA, scCB2, scDblFinder, scDD, scds, scHOT, scmap, scMerge, scmeth, SCnorm, scoreInvHap, scp, scPipe, scran, scRepertoire, scRNAseq, scruff, scry, scTensor, scTGIF, scuttle, sechm, seqCAT, sesame, SEtools, sigFeature, SigsPack, SingleCellMultiModal, singscore, SingscoreAMLMutations, slalom, slingshot, slinky, snapcount, SNPhood, Spaniel, SpatialCPie, SpatialExperiment, spatialHeatmap, spatialLIBD, splatter, SplicingFactory, srnadiff, struct, StructuralVariantAnnotation, supersigs, switchde, systemPipeR, systemPipeTools, TBSignatureProfiler, TCGAbiolinks, TCGAbiolinksGUI, TCGAutils, TCGAWorkflow, TCGAWorkflowData, TCseq, tenXplore, tidybulk, tidySingleCellExperiment, TOAST, tomoda, ToPASeq, ToxicoGx, tradeSeq, TrajectoryUtils, TraRe, TreeSummarizedExperiment, Trendy, tricycle, TSCAN, tscR, TSRchitect, TTMap, TVTB, tximeta, VariantFiltering, vidger, wpm, xcms, zellkonverter, zFPKM |
| Suggests Me |
AnnotationHub, biobroom, BiocPkgTools, biotmleData, CAGEWorkflow, curatedAdipoArray, dcanr, dce, dearseq, DelayedArray, dorothea, DuoClustering2018, edgeR, EnMCB, epivizr, epivizrChart, esetVis, fobitools, GENIE3, GenomicRanges, globalSeq, gsean, HDF5Array, Informeasure, InteractiveComplexHeatmap, interactiveDisplay, MatrixGenerics, mistyR, MOFA2, MSnbase, pathwayPCA, podkat, PubScore, RforProteomics, RiboProfiling, S4Vectors, SBGNview.data, scFeatureFilter, semisup, systemPipeShiny, TFutils, tissueTreg |
| Links To Me |
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| Build Report |
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