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.
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| biocViews |
Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software |
| Version |
1.18.2 |
| In Bioconductor since |
BioC 3.2 (R-3.2) (5 years) |
| License |
Artistic-2.0 |
| Depends |
R (>= 3.2), methods, GenomicRanges(>= 1.33.6), Biobase, DelayedArray(>= 0.3.20) |
| Imports |
utils, stats, tools, Matrix, BiocGenerics(>= 0.15.3), S4Vectors(>= 0.25.14), IRanges(>= 2.21.6), GenomeInfoDb(>= 1.13.1) |
| LinkingTo |
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| Suggests |
annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown, digest, jsonlite, rhdf5, HDF5Array(>= 1.7.5), airway, RUnit, testthat |
| SystemRequirements |
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| Enhances |
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| URL |
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| Depends On Me |
AffiXcan, airway, AllelicImbalance, ASpediaFI, BDMMAcorrect, benchmarkfdrData2019, BiocSklearn, BiSeq, bnbc, bodymapRat, bsseq, CAGEfightR, celaref, 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, 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, lipidr, LoomExperiment, MBASED, MetaGxBreast, MetaGxOvarian, methrix, methylPipe, microRNAome, minfi, miRmine, MouseGastrulationData, mpra, MultiAssayExperiment, NADfinder, NBAMSeq, OUTRIDER, parathyroidSE, PowerExplorer, profileplyr, recount, REMP, restfulSE, restfulSEData, RIPSeeker, ROCpAI, rqt, runibic, sampleClassifierData, Scale4C, scGPS, scone, SDAMS, SGSeq, signatureSearch, simulatorZ, SingleCellExperiment, singleCellTK, SingleR, soGGi, Spaniel, spqn, spqnData, sRACIPE, ssPATHS, stageR, SummarizedBenchmark, survtype, TimeSeriesExperiment, TissueEnrich, TNBC.CMS, VanillaICE, VariantAnnotation, VariantExperiment, weitrix, yamss, zinbwave |
| Imports Me |
ADAM, adaptest, ALDEx2, alpine, anamiR, animalcules, anota2seq, APAlyzer, apeglm, appreci8R, ASICS, AUCell, BASiCS, batchelor, bayNorm, BBCAnalyzer, bigPint, BiocOncoTK, biotmle, biovizBase, biscuiteer, BiSeq, blacksheepr, BloodCancerMultiOmics2017, brgedata, BRGenomics, BUMHMM, BUScorrect, CAGEr, CAMTHC, CATALYST, cBioPortalData, ccfindR, celda, CellMixS, CellTrails, CeTF, CHARGE, CHETAH, ChIPpeakAnno, chromVAR, CiteFuse, CLLmethylation, clustifyr, cmapR, CNVfilteR, CNVRanger, coexnet, CoGAPS, combi, compartmap, consensusDE, CopyNumberPlots, CoreGx, COSMIC.67, countsimQC, curatedTCGAData, cydar, cytomapper, DAMEfinder, DChIPRep, debCAM, debrowser, DEComplexDisease, decompTumor2Sig, DEFormats, DEGreport, deltaCaptureC, DEP, DEScan2, destiny, DEWSeq, diffcyt, DiscoRhythm, distinct, dittoSeq, DominoEffect, doppelgangR, doseR, Dune, easyRNASeq, eisaR, ELMER, ensemblVEP, epivizrData, erma, FCBF, fcScan, fishpond, fluentGenomics, FourCSeq, GARS, gCrisprTools, GeneTonic, GenomicDataCommons, GGBase, ggbio, glmGamPoi, glmSparseNet, GNET2, gQTLBase, gQTLstats, gramm4R, GreyListChIP, gscreend, GSVA, gwasurvivr, HMP2Data, HTSeqGenie, HumanTranscriptomeCompendium, iasva, icetea, ideal, IHWpaper, ImpulseDE2, infercnv, INSPEcT, InterMineR, iSEEu, iteremoval, LACE, LineagePulse, lionessR, M3D, MADSEQ, MAST, mbkmeans, MBQN, mCSEA, MEAL, MEAT, MEB, MetaGxPancreas, MetaNeighbor, metaseqR2, methyAnalysis, MethylAid, methylumi, methyvim, MinimumDistance, miRLAB, miRSM, missMethyl, MLSeq, MoonlightR, motifbreakR, motifmatchr, MPRAnalyze, msgbsR, MTseeker, MultiDataSet, multiOmicsViz, muscat, MutationalPatterns, MWASTools, netSmooth, NoRCE, NormalyzerDE, oligoClasses, omicRexposome, OmicsLonDA, omicsPrint, oncomix, ORFik, OVESEG, PAIRADISE, pcaExplorer, peco, PharmacoGx, phemd, phenopath, pmp, proDA, psichomics, pulsedSilac, PureCN, qsmooth, R453Plus1Toolbox, RaggedExperiment, RareVariantVis, RcisTarget, readat, receptLoss, regionReport, regsplice, rgsepd, Rmmquant, RNAAgeCalc, RNAsense, roar, rScudo, RTCGAToolbox, RTN, SBGNview, SC3, scater, scBFA, scDblFinder, scDD, scds, scfind, scHOT, scmap, scMerge, scmeth, SCnorm, scoreInvHap, scPipe, scran, scRNAseq, scruff, scry, scTensor, scTGIF, seqCAT, sesame, SEtools, sigFeature, SigsPack, singscore, SingscoreAMLMutations, slalom, slingshot, slinky, snapcount, SNPhood, SpatialCPie, spatialLIBD, splatter, srnadiff, struct, SVAPLSseq, switchde, systemPipeR, TBSignatureProfiler, TCGAbiolinks, TCGAbiolinksGUI, TCGAutils, TCGAWorkflow, TCGAWorkflowData, TCseq, tenXplore, TOAST, ToPASeq, tradeSeq, TreeSummarizedExperiment, Trendy, tscR, TSRchitect, TTMap, TVTB, tximeta, TxRegInfra, VariantFiltering, vidger, xcms, yriMulti, zFPKM |
| Suggests Me |
AnnotationHub, biobroom, biotmleData, CAGEWorkflow, curatedAdipoArray, dcanr, dearseq, DelayedArray, dorothea, DuoClustering2018, edgeR, EnMCB, epivizr, epivizrChart, esetVis, GENIE3, GenomicRanges, Glimma, globalSeq, gsean, HDF5Array, interactiveDisplay, methyvimData, MSnbase, pathprint, pathprintGEOData, pathwayPCA, podkat, PubScore, RforProteomics, RiboProfiling, S4Vectors, SBGNview.data, scFeatureFilter, semisup, StructuralVariantAnnotation, TFutils, tidybulk, tissueTreg |
| Links To Me |
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| Build Report |
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