SummarizedExperiment

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see SummarizedExperiment.

SummarizedExperiment container

Bioconductor version: 3.7

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 bioconductor.org>

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

Installation

To install this package, start R (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SummarizedExperiment")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SummarizedExperiment")

SummarizedExperiment	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software
Version	1.10.1
In Bioconductor since	BioC 3.2 (R-3.2) (8.5 years)
License	Artistic-2.0
Depends	R (>= 3.2), methods, GenomicRanges(>= 1.31.17), Biobase, DelayedArray(>= 0.3.20)
Imports	utils, stats, tools, Matrix, BiocGenerics(>= 0.15.3), S4Vectors(>= 0.17.25), IRanges(>= 2.13.16), GenomeInfoDb(>= 1.13.1)
System Requirements
URL

Suggests	annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown, digest, jsonlite, rhdf5, HDF5Array(>= 1.7.5), airway, RUnit
Linking To
Enhances
Depends On Me	airway, AllelicImbalance, anamiR, BiocSklearn, BiSeq, bnbc, bsseq, CAGEfightR, clusterExperiment, coseq, csaw, cydar, DaMiRseq, deepSNV, DESeq2, DEXSeq, DiffBind, diffcoexp, diffHic, DMCHMM, DREAM4, dsQTL, ENmix, EnrichmentBrowser, epigenomix, EventPointer, ExpressionAtlas, fission, GenoGAM, GenomicAlignments, GenomicFiles, genoset, geuvPack, GRmetrics, GSEABenchmarkeR, HDCytoData, HelloRanges, hipathia, HMP16SData, InTAD, InteractionSet, IntEREst, iSEE, isomiRs, ivygapSE, JunctionSeq, MBASED, methylPipe, microRNAome, minfi, miRmine, mpra, NADfinder, parathyroidSE, PowerExplorer, recount, REMP, restfulSE, restfulSEData, RIPSeeker, rqt, runibic, sampleClassifierData, Scale4C, scater, scone, scRNAseq, SDAMS, SGSeq, simulatorZ, SingleCellExperiment, singleCellTK, soGGi, stageR, SummarizedBenchmark, TissueEnrich, VanillaICE, VariantAnnotation, yamss, zinbwave
Imports Me	adaptest, ALDEx2, alpine, anamiR, anota2seq, apeglm, ASICS, AUCell, BASiCS, BBCAnalyzer, biotmle, biovizBase, BiSeq, BloodCancerMultiOmics2017, brgedata, BUMHMM, CAGEr, CATALYST, ccfindR, CHARGE, ChIPpeakAnno, chromVAR, CLLmethylation, CNPBayes, coexnet, COSMIC.67, DChIPRep, debrowser, DEComplexDisease, DEFormats, DEGreport, DEP, DEScan2, destiny, diffcyt, DominoEffect, easyRNASeq, ELMER, ensemblVEP, epivizrData, erma, FourCSeq, GARS, GenomicDataCommons, GGBase, ggbio, gQTLBase, gQTLstats, GreyListChIP, gwascat, HTSeqGenie, ideal, IHWpaper, ImpulseDE2, InterMineR, iteremoval, LineagePulse, M3D, MADSEQ, MAST, mCSEA, MEAL, MetaNeighbor, methyAnalysis, MethylAid, methylumi, methyvim, MinimumDistance, MLSeq, MoonlightR, motifmatchr, msgbsR, MultiAssayExperiment, MultiDataSet, multiOmicsViz, MutationalPatterns, MWASTools, netSmooth, oligoClasses, omicRexposome, omicsPrint, oncomix, pcaExplorer, phenopath, psichomics, PureCN, R453Plus1Toolbox, RaggedExperiment, RareVariantVis, RcisTarget, readat, regionReport, regsplice, rgsepd, roar, RTCGAToolbox, SC3, scDD, scfind, scmap, scmeth, SCnorm, scoreInvHap, scPipe, scran, semisup, seqCAT, singscore, slalom, SNPchip, SNPhood, splatter, srnadiff, SVAPLSseq, switchde, systemPipeR, TCGAbiolinks, TCGAbiolinksGUI, TCGAutils, TCGAWorkflow, TCGAWorkflowData, TCseq, tenXplore, Trendy, TSRchitect, TTMap, TVTB, TxRegInfra, VariantFiltering, vidger, yriMulti, zFPKM
Suggests Me	AnnotationHub, biobroom, biotmleData, DelayedArray, epivizr, epivizrChart, esetVis, GENIE3, GenomicRanges, Glimma, globalSeq, HDF5Array, interactiveDisplay, methyvimData, MSnbase, pathprint, pathprintGEOData, podkat, RforProteomics, RiboProfiling, S4Vectors, scFeatureFilter, TFutils, tissueTreg
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SummarizedExperiment_1.10.1.tar.gz
Windows Binary	SummarizedExperiment_1.10.1.zip
Mac OS X 10.11 (El Capitan)	SummarizedExperiment_1.10.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SummarizedExperiment
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SummarizedExperiment
Package Short Url	https://bioconductor.org/packages/SummarizedExperiment/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.7	Source Archive