This package is for version 3.12 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 |
1.20.0 |
In Bioconductor since |
BioC 3.2 (R-3.2) (5.5 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) |
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, 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 |
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Build Report |
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