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.
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 |
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Suggests |
annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown, digest, jsonlite, rhdf5, HDF5Array(>= 1.7.5), airway, RUnit |
SystemRequirements |
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Enhances |
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URL |
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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 |
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