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 (3.9)

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 "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("SummarizedExperiment", version = "3.9")

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")

 

HTML R Script 1. SummarizedExperiment for Coordinating Experimental Assays, Samples, and Regions of Interest
HTML R Script 2. Extending the SummarizedExperiment class
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software
Version 1.13.0
In Bioconductor since BioC 3.2 (R-3.2) (3 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(>= 0.17.25), 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, testthat
SystemRequirements
Enhances
URL
Depends On Me AffiXcan, airway, AllelicImbalance, BDMMAcorrect, BiocSklearn, BiSeq, bnbc, bsseq, CAGEfightR, celaref, coseq, csaw, DaMiRseq, deepSNV, DESeq2, DEXSeq, DiffBind, diffcoexp, diffHic, DMCHMM, DREAM4, dsQTL, ENmix, EnrichmentBrowser, epigenomix, EventPointer, ExpressionAtlas, fission, FlowSorted.Blood.EPIC, GenoGAM, GenomicAlignments, GenomicFiles, genoset, geuvPack, GRmetrics, GSEABenchmarkeR, HDCytoData, HelloRanges, hipathia, HMP16SData, InTAD, InteractionSet, IntEREst, iSEE, isomiRs, ivygapSE, JunctionSeq, LoomExperiment, MBASED, methylPipe, microRNAome, minfi, miRmine, mpra, MultiAssayExperiment, NADfinder, OUTRIDER, parathyroidSE, PowerExplorer, recount, REMP, restfulSE, restfulSEData, RIPSeeker, rqt, runibic, sampleClassifierData, Scale4C, scone, scRNAseq, SDAMS, SGSeq, simulatorZ, SingleCellExperiment, singleCellTK, soGGi, stageR, SummarizedBenchmark, TimeSeriesExperiment, TissueEnrich, VanillaICE, VariantAnnotation, yamss, zinbwave
Imports Me adaptest, ALDEx2, alpine, anamiR, anota2seq, apeglm, appreci8R, ASICS, AUCell, BASiCS, bayNorm, BBCAnalyzer, BiocOncoTK, biotmle, biovizBase, BiSeq, BloodCancerMultiOmics2017, brgedata, BUMHMM, BUScorrect, CAGEr, CAMTHC, CATALYST, ccfindR, CellTrails, CHARGE, ChIPpeakAnno, chromVAR, CLLmethylation, CNPBayes, coexnet, CoGAPS, compartmap, consensusDE, COSMIC.67, countsimQC, cydar, DChIPRep, debrowser, DEComplexDisease, DEFormats, DEGreport, DEP, DEScan2, destiny, diffcyt, DominoEffect, doppelgangR, easyRNASeq, ELMER, ensemblVEP, epivizrData, erma, FCBF, FourCSeq, GARS, GenomicDataCommons, GGBase, ggbio, glmSparseNet, gQTLBase, gQTLstats, GreyListChIP, gwascat, gwasurvivr, HTSeqGenie, iasva, icetea, ideal, IHWpaper, ImpulseDE2, InterMineR, iteremoval, LineagePulse, M3D, MADSEQ, mCSEA, MEAL, MetaNeighbor, methyAnalysis, MethylAid, methylumi, methyvim, MinimumDistance, miRLAB, miRSM, MLSeq, MoonlightR, motifmatchr, MPRAnalyze, msgbsR, MTseeker, MultiDataSet, multiOmicsViz, MutationalPatterns, MWASTools, NormalyzerDE, oligoClasses, omicRexposome, omicsPrint, oncomix, pcaExplorer, phenopath, psichomics, PureCN, R453Plus1Toolbox, RaggedExperiment, RareVariantVis, RcisTarget, readat, regionReport, regsplice, rgsepd, Rmmquant, roar, RTCGAToolbox, SC3, scater, scDD, scfind, scmap, scmeth, SCnorm, scoreInvHap, scPipe, scran, scruff, semisup, seqCAT, sigFeature, singscore, slalom, slinky, SNPchip, SNPhood, splatter, srnadiff, SVAPLSseq, switchde, systemPipeR, TCGAbiolinks, TCGAbiolinksGUI, TCGAutils, TCGAWorkflowData, TCseq, tenXplore, Trendy, TSRchitect, TTMap, TVTB, tximeta, TxRegInfra, VariantFiltering, vidger, yriMulti, zFPKM
Suggests Me AnnotationHub, biobroom, biotmleData, DelayedArray, DuoClustering2018, epivizr, epivizrChart, esetVis, GENIE3, GenomicRanges, Glimma, globalSeq, HDF5Array, interactiveDisplay, methyvimData, MSnbase, pathprint, pathprintGEOData, podkat, RiboProfiling, S4Vectors, scFeatureFilter, sesame, TFutils, tissueTreg
Links To Me
Build Report  

Package Archives

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

Source Package SummarizedExperiment_1.13.0.tar.gz
Windows Binary SummarizedExperiment_1.13.0.zip
Mac OS X 10.11 (El Capitan) SummarizedExperiment_1.13.0.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 http://bioconductor.org/packages/SummarizedExperiment/
Package Downloads Report Download Stats

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