To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

SummarizedExperiment

 

   

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

SummarizedExperiment container

Bioconductor version: Development (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 bioconductor.org>

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

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 1.5.7
In Bioconductor since BioC 3.2 (R-3.2) (1.5 years)
License Artistic-2.0
Depends R (>= 3.2), methods, GenomicRanges(>= 1.27.22), Biobase, DelayedArray(>= 0.1.6)
Imports utils, stats, Matrix, BiocGenerics(>= 0.15.3), S4Vectors(>= 0.13.13), IRanges(>= 2.7.2), GenomeInfoDb(>= 1.11.4)
LinkingTo
Suggests annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown, digest, jsonlite, rhdf5, HDF5Array(>= 1.3.7), airway, RUnit
SystemRequirements
Enhances
URL
Depends On Me airway, AllelicImbalance, anamiR, BiSeq, bsseq, clusterExperiment, coseq, csaw, deepSNV, DESeq2, DEXSeq, DiffBind, diffHic, DREAM4, dsQTL, epigenomix, EventPointer, ExpressionAtlas, fission, GenoGAM, GenomicAlignments, GenomicFiles, genoset, geuvPack, GRmetrics, HelloRanges, InteractionSet, isomiRs, JunctionSeq, MAST, MBASED, methylPipe, minfi, parathyroidSE, recount, RIPSeeker, sampleClassifierData, scone, scRNAseq, SGSeq, simulatorZ, soGGi, VanillaICE, VariantAnnotation, yamss, yriMulti
Imports Me ALDEx2, alpine, anamiR, BBCAnalyzer, biovizBase, BiSeq, BUMHMM, ChIPpeakAnno, CNPBayes, COSMIC.67, DChIPRep, debrowser, DEFormats, easyRNASeq, EnrichmentBrowser, ensemblVEP, epivizrData, erma, FourCSeq, GGBase, ggbio, gQTLBase, gQTLstats, GreyListChIP, gwascat, HTSeqGenie, IHWpaper, M3D, MADSEQ, methyAnalysis, methylumi, MinimumDistance, MoonlightR, MultiAssayExperiment, MultiDataSet, MutationalPatterns, MWASTools, oligoClasses, pcaExplorer, PureCN, R453Plus1Toolbox, readat, regionReport, regsplice, REMP, rgsepd, roar, scDD, SeqArray, SNPchip, SNPhood, SVAPLSseq, systemPipeR, TCGAbiolinks, TCGAbiolinksGUI, TCseq, ToPASeq, TVTB, VariantFiltering
Suggests Me AnnotationHub, biobroom, epivizr, esetVis, GenomicRanges, globalSeq, HDF5Array, interactiveDisplay, podkat, RiboProfiling, splatter
Build Report  

Package Archives

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

Package Source SummarizedExperiment_1.5.7.tar.gz
Windows Binary SummarizedExperiment_1.5.7.zip
Mac OS X 10.9 (Mavericks) SummarizedExperiment_1.5.7.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/SummarizedExperiment
Package Short Url http://bioconductor.org/packages/SummarizedExperiment/
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