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DOI: 10.18129/B9.bioc.SummarizedExperiment    

SummarizedExperiment container

Bioconductor version: Release (3.5)

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>

Citation (from within R, enter citation("SummarizedExperiment")):


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HTML R Script SummarizedExperiment
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biocViews Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software
Version 1.6.5
In Bioconductor since BioC 3.2 (R-3.2) (2 years)
License Artistic-2.0
Depends R (>= 3.2), methods, GenomicRanges(>= 1.27.22), Biobase, DelayedArray(>= 0.1.9)
Imports utils, stats, tools, Matrix, BiocGenerics(>= 0.15.3), S4Vectors(>= 0.13.13), IRanges(>= 2.7.2), GenomeInfoDb(>= 1.11.4)
Suggests annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown, digest, jsonlite, rhdf5, HDF5Array(>= 1.4.8), airway, RUnit
Depends On Me airway, AllelicImbalance, anamiR, BiSeq, bsseq, clusterExperiment, coseq, csaw, cydar, DaMiRseq, deepSNV, DESeq2, DEXSeq, DiffBind, diffHic, DREAM4, dsQTL, ENmix, epigenomix, EventPointer, ExpressionAtlas, fission, GenoGAM, GenomicAlignments, GenomicFiles, genoset, geuvPack, GRmetrics, HelloRanges, InteractionSet, IntEREst, isomiRs, JunctionSeq, MAST, MBASED, methylPipe, minfi, parathyroidSE, recount, REMP, RIPSeeker, rqt, sampleClassifierData, scone, scRNAseq, SGSeq, simulatorZ, soGGi, VanillaICE, VariantAnnotation, yamss, yriMulti
Imports Me ALDEx2, alpine, anamiR, BBCAnalyzer, biotmle, biovizBase, BiSeq, BUMHMM, ChIPpeakAnno, CNPBayes, COSMIC.67, DChIPRep, debrowser, DEFormats, easyRNASeq, EnrichmentBrowser, ensemblVEP, epivizrData, erma, FourCSeq, GGBase, ggbio, gQTLBase, gQTLstats, GreyListChIP, gwascat, HTSeqGenie, ideal, IHWpaper, ImpulseDE2, M3D, MADSEQ, methyAnalysis, MethylAid, methylumi, MinimumDistance, MoonlightR, msgbsR, MultiAssayExperiment, MultiDataSet, multiOmicsViz, MutationalPatterns, MWASTools, NADfinder, oligoClasses, pcaExplorer, PureCN, R453Plus1Toolbox, RaggedExperiment, RareVariantVis, readat, regionReport, regsplice, rgsepd, roar, scDD, semisup, SeqArray, SNPchip, SNPhood, SVAPLSseq, systemPipeR, TCGAbiolinks, TCGAbiolinksGUI, TCGAWorkflowData, TCseq, ToPASeq, TSRchitect, TVTB, VariantFiltering
Suggests Me AnnotationHub, biobroom, biotmleData, epivizr, esetVis, GenomicRanges, globalSeq, HDF5Array, interactiveDisplay, pathprint, pathprintGEOData, podkat, RiboProfiling, splatter
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