SummarizedExperiment

DOI: 10.18129/B9.bioc.SummarizedExperiment    

This is the development version of SummarizedExperiment; for the stable release version, see SummarizedExperiment.

SummarizedExperiment container

Bioconductor version: Development (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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SummarizedExperiment")

Documentation

HTML	R Script	SummarizedExperiment
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software
Version	1.9.16
In Bioconductor since	BioC 3.2 (R-3.2) (2.5 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)
LinkingTo
Suggests	annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown, digest, jsonlite, rhdf5, HDF5Array(>= 1.7.5), airway, RUnit
SystemRequirements
Enhances
URL
Depends On Me	airway, AllelicImbalance, anamiR, BiocSklearn, BiSeq, bnbc, bsseq, 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, 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, GGBase, ggbio, gQTLBase, gQTLstats, GreyListChIP, gwascat, HTSeqGenie, ideal, IHWpaper, ImpulseDE2, InterMineR, iteremoval, LineagePulse, M3D, MADSEQ, MAST, mCSEA, MEAL, MetaNeighbor, methyAnalysis, MethylAid, methylumi, methyvim, MinimumDistance, MoonlightR, motifmatchr, msgbsR, MultiAssayExperiment, MultiDataSet, multiOmicsViz, MutationalPatterns, MWASTools, oligoClasses, omicRexposome, omicsPrint, oncomix, pcaExplorer, phenopath, PureCN, R453Plus1Toolbox, RaggedExperiment, RareVariantVis, RcisTarget, readat, regionReport, regsplice, rgsepd, roar, RTCGAToolbox, SC3, scDD, scfind, scmap, scmeth, SCnorm, scoreInvHap, scPipe, scran, semisup, seqCAT, slalom, SNPchip, SNPhood, splatter, srnadiff, SVAPLSseq, switchde, systemPipeR, TCGAbiolinks, TCGAbiolinksGUI, TCGAWorkflow, TCGAWorkflowData, TCseq, tenXplore, Trendy, TSRchitect, TTMap, TVTB, 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
Build Report

Package Archives

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

Source Package	SummarizedExperiment_1.9.16.tar.gz
Windows Binary	SummarizedExperiment_1.9.16.zip
Mac OS X 10.11 (El Capitan)	SummarizedExperiment_1.9.16.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SummarizedExperiment
Package Short Url	http://bioconductor.org/packages/SummarizedExperiment/
Package Downloads Report	Download Stats