This package is for version 3.10 of Bioconductor;
for the stable, up-to-date release version, see
SummarizedExperiment.
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.
To view documentation for the version of this package installed
in your system, start R and enter:
| biocViews |
Annotation, Coverage, Genetics, GenomeAnnotation, Infrastructure, Sequencing, Software |
| Version |
1.16.1 |
| In Bioconductor since |
BioC 3.2 (R-3.2) (4.5 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(>= 0.23.20), 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, testthat |
| SystemRequirements |
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| Enhances |
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| URL |
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| Depends On Me |
AffiXcan, airway, AllelicImbalance, ASpediaFI, BDMMAcorrect, benchmarkfdrData2019, BiocSklearn, BiSeq, bnbc, bodymapRat, bsseq, CAGEfightR, celaref, clusterExperiment, coseq, csaw, curatedAdipoChIP, curatedAdipoRNA, DaMiRseq, deco, deepSNV, DeMixT, DESeq2, DEXSeq, DiffBind, diffcoexp, diffHic, divergence, DMCFB, DMCHMM, DMRcate, DREAM4, dsQTL, ENmix, EnrichmentBrowser, epigenomix, evaluomeR, EventPointer, ExpressionAtlas, fission, FlowSorted.Blood.EPIC, FlowSorted.CordBloodCombined.450k, GenoGAM, GenomicAlignments, GenomicFiles, genoset, geuvPack, GRmetrics, GSEABenchmarkeR, HDCytoData, HelloRanges, hipathia, HMP16SData, IgGeneUsage, InTAD, InteractionSet, IntEREst, iSEE, isomiRs, ivygapSE, JunctionSeq, lipidr, LoomExperiment, MBASED, MetaGxBreast, MetaGxOvarian, methrix, methylPipe, microRNAome, minfi, miRmine, mpra, MultiAssayExperiment, NADfinder, NBAMSeq, OUTRIDER, parathyroidSE, PowerExplorer, profileplyr, recount, REMP, restfulSE, restfulSEData, RIPSeeker, rqt, runibic, sampleClassifierData, Scale4C, scGPS, scone, SDAMS, SGSeq, signatureSearch, simulatorZ, SingleCellExperiment, singleCellTK, SingleR, soGGi, Spaniel, sRACIPE, ssPATHS, stageR, SummarizedBenchmark, survtype, TimeSeriesExperiment, TissueEnrich, TNBC.CMS, VanillaICE, VariantAnnotation, VariantExperiment, yamss, zinbwave |
| Imports Me |
ADAM, adaptest, ALDEx2, alpine, anamiR, animalcules, anota2seq, APAlyzer, apeglm, appreci8R, ASICS, AUCell, BASiCS, batchelor, bayNorm, BBCAnalyzer, BiocOncoTK, biotmle, biovizBase, biscuiteer, BiSeq, blacksheepr, BloodCancerMultiOmics2017, brgedata, BUMHMM, BUScorrect, CAGEr, CAMTHC, CATALYST, ccfindR, celda, CellMixS, CellTrails, CHARGE, CHETAH, ChIPpeakAnno, chromVAR, CLLmethylation, CNVfilteR, CNVRanger, coexnet, CoGAPS, compartmap, consensusDE, CopyNumberPlots, COSMIC.67, countsimQC, curatedTCGAData, cydar, DChIPRep, debCAM, debrowser, DEComplexDisease, decompTumor2Sig, DEFormats, DEGreport, deltaCaptureC, DEP, DEScan2, destiny, DEWSeq, diffcyt, DiscoRhythm, DominoEffect, doppelgangR, doseR, easyRNASeq, ELMER, ensemblVEP, epivizrData, erma, FCBF, fcScan, fishpond, FourCSeq, GARS, GenomicDataCommons, GGBase, ggbio, glmSparseNet, GNET2, gQTLBase, gQTLstats, gramm4R, GreyListChIP, gscreend, gwasurvivr, HMP2Data, HTSeqGenie, HumanTranscriptomeCompendium, iasva, icetea, ideal, IHWpaper, ImpulseDE2, infercnv, INSPEcT, InterMineR, iteremoval, LineagePulse, lionessR, M3D, MADSEQ, MAST, mbkmeans, MBQN, mCSEA, MEAL, MEB, MetaGxPancreas, MetaNeighbor, methyAnalysis, MethylAid, methylumi, methyvim, MinimumDistance, miRLAB, miRSM, MLSeq, MoonlightR, motifbreakR, motifmatchr, MPRAnalyze, msgbsR, MTseeker, MultiDataSet, multiOmicsViz, muscat, MutationalPatterns, MWASTools, netSmooth, NormalyzerDE, oligoClasses, omicRexposome, OmicsLonDA, omicsPrint, oncomix, ORFik, OVESEG, PAIRADISE, pcaExplorer, phemd, phenopath, proDA, psichomics, pulsedSilac, PureCN, qsmooth, R453Plus1Toolbox, RaggedExperiment, RareVariantVis, RcisTarget, readat, regionReport, regsplice, rgsepd, Rmmquant, RNAsense, roar, rScudo, RTCGAToolbox, RTN, SBGNview, SC3, scater, scBFA, scDblFinder, scDD, scds, scfind, scmap, scMerge, scmeth, SCnorm, scoreInvHap, scPipe, scran, scRNAseq, scruff, scTensor, scTGIF, seqCAT, SEtools, sigFeature, SigsPack, singscore, SingscoreAMLMutations, slalom, slingshot, slinky, SNPchip, SNPhood, SpatialCPie, splatter, srnadiff, SVAPLSseq, switchde, systemPipeR, TCGAbiolinks, TCGAbiolinksGUI, TCGAutils, TCGAWorkflow, TCGAWorkflowData, TCseq, tenXplore, TOAST, ToPASeq, tradeSeq, TreeSummarizedExperiment, Trendy, TSRchitect, TTMap, TVTB, tximeta, TxRegInfra, VariantFiltering, vidger, yriMulti, zFPKM |
| Suggests Me |
AnnotationHub, biobroom, biotmleData, CAGEWorkflow, dcanr, DelayedArray, DuoClustering2018, epivizr, epivizrChart, esetVis, GENIE3, GenomicRanges, Glimma, globalSeq, gsean, HDF5Array, interactiveDisplay, methyvimData, MSnbase, pathprint, pathprintGEOData, pathwayPCA, podkat, RforProteomics, RiboProfiling, S4Vectors, SBGNview.data, scFeatureFilter, semisup, sesame, StructuralVariantAnnotation, TFutils, tissueTreg |
| Links To Me |
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| Build Report |
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