This package is for version 3.17 of Bioconductor;
for the stable, up-to-date release version, see
limma.
Data analysis, linear models and differential expression for microarray data.
Author: Gordon Smyth [cre,aut], Yifang Hu [ctb], Matthew Ritchie [ctb], Jeremy Silver [ctb], James Wettenhall [ctb], Davis McCarthy [ctb], Di Wu [ctb], Wei Shi [ctb], Belinda Phipson [ctb], Aaron Lun [ctb], Natalie Thorne [ctb], Alicia Oshlack [ctb], Carolyn de Graaf [ctb], Yunshun Chen [ctb], Mette Langaas [ctb], Egil Ferkingstad [ctb], Marcus Davy [ctb], Francois Pepin [ctb], Dongseok Choi [ctb]
To view documentation for the version of this package installed
in your system, start R and enter:
| biocViews |
AlternativeSplicing, BatchEffect, Bayesian, BiomedicalInformatics, CellBiology, Cheminformatics, Clustering, DataImport, DifferentialExpression, DifferentialSplicing, Epigenetics, ExonArray, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Metabolomics, MicroRNAArray, Microarray, MultipleComparison, Normalization, OneChannel, Preprocessing, ProprietaryPlatforms, Proteomics, QualityControl, RNASeq, Regression, Sequencing, Software, SystemsBiology, TimeCourse, Transcription, Transcriptomics, TwoChannel, mRNAMicroarray |
| Version |
3.56.2 |
| In Bioconductor since |
BioC 1.6 (R-2.1) or earlier (> 18.5 years) |
| License |
GPL (>=2) |
| Depends |
R (>= 3.6.0) |
| Imports |
grDevices, graphics, stats, utils, methods |
| LinkingTo |
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| Suggests |
affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db, gplots, illuminaio, locfit, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn |
| SystemRequirements |
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| Enhances |
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| URL |
https://bioinf.wehi.edu.au/limma/ |
| Depends On Me |
AgiMicroRna, ASpli, BLMA, CCl4, cghMCR, ChimpHumanBrainData, clippda, codelink, convert, Cormotif, deco, DEqMS, DrugVsDisease, edgeR, EGSEA123, ExiMiR, ExpressionAtlas, Fletcher2013a, GEOexplorer, HD2013SGI, HTqPCR, IsoformSwitchAnalyzeR, maEndToEnd, maigesPack, maPredictDSC, marray, metagenomeSeq, metaseqR2, methylationArrayAnalysis, mpra, NanoTube, NeuCA, octad, protGear, qpcrNorm, qusage, RBM, ReactomeGSA.data, Ringo, RNAseq123, RnBeads, Rnits, splineTimeR, TOAST, tRanslatome, TurboNorm, variancePartition, wateRmelon, zenith |
| Imports Me |
a4Base, ABSSeq, affycoretools, affylmGUI, AMARETTO, animalcules, anota2seq, ArrayExpress, arrayQuality, arrayQualityMetrics, artMS, ASpediaFI, ATACseqQC, ATACseqTFEA, attract, autonomics, AWFisher, ballgown, BatchQC, beadarray, BeadArrayUseCases, benchdamic, biotmle, BloodGen3Module, bnem, bsseq, BubbleTree, bumphunter, CancerSubtypes, casper, ChAMP, ChIPComp, clusterExperiment, CNVRanger, combi, compcodeR, CONFESS, consensusDE, consensusOV, crlmm, crossmeta, csaw, cTRAP, ctsGE, DAMEfinder, DaMiRseq, debrowser, DELocal, DEP, derfinderPlot, DESpace, DEsubs, DExMA, DiffBind, diffcyt, diffHic, diffUTR, distinct, DmelSGI, DMRcate, Doscheda, DRIMSeq, eegc, EGAD, EGSEA, eisaR, EnrichmentBrowser, epigraHMM, EpiMix, erccdashboard, EventPointer, EWCE, ExpHunterSuite, ExploreModelMatrix, ExpressionNormalizationWorkflow, extraChIPs, flowBin, gCrisprTools, GDCRNATools, genefu, GeneSelectMMD, GEOquery, Glimma, GOsummaries, GRaNIE, GUIDEseq, GWAS.BAYES, hermes, hipathia, HTqPCR, icetea, iCheck, iChip, iCOBRA, ideal, InPAS, isomiRs, KnowSeq, limmaGUI, Linnorm, lipidr, lmdme, mAPKL, mastR, MatrixQCvis, MBECS, MBQN, mCSEA, MEAL, methylKit, MethylMix, microbiomeExplorer, microbiomeMarker, MIGSA, miloR, minfi, miRLAB, missMethyl, MLSeq, moanin, monocle, MoonlightR, msImpute, msqrob2, MSstats, MSstatsTMT, MultiDataSet, muscat, NADfinder, NanoMethViz, nethet, nondetects, NormalyzerDE, OLIN, omicRexposome, oppti, OVESEG, PAA, PADOG, pairedGSEA, PanomiR, PathoStat, pcaExplorer, PECA, pepStat, phantasus, phenomis, phenoTest, PhosR, polyester, POMA, POWSC, projectR, psichomics, pwrEWAS, qmtools, qPLEXanalyzer, qsea, rCGH, recountWorkflow, RegEnrich, regsplice, ReportingTools, Ringo, RNAinteract, ROSeq, RTN, RTopper, satuRn, scClassify, scone, scran, ScreenR, scviR, SEPIRA, seqsetvis, shinyepico, signatureSearchData, SimBindProfiles, SingleCellSignalR, singleCellTK, snapCGH, sparrow, spatialLIBD, speckle, SPsimSeq, standR, STATegRa, Statial, sva, timecourse, TOP, ToxicoGx, TPP, TPP2D, transcriptogramer, TVTB, tweeDEseq, vsclust, vsn, weitrix, Wrench, yamss, yarn |
| Suggests Me |
ABarray, ADaCGH2, arrays, beadarraySNP, biobroom, BiocSet, BioNet, BioQC, BloodCancerMultiOmics2017, CAGEWorkflow, Category, categoryCompare, celaref, CellBench, CellMixS, ChIPpeakAnno, ClassifyR, CMA, coGPS, CONSTANd, cydar, DAPAR, dearseq, DEGreport, derfinder, DEScan2, dyebias, easyreporting, EnMCB, fgsea, fishpond, fluentGenomics, gage, GeoTcgaData, GeuvadisTranscriptExpr, geva, glmGamPoi, GSRI, GSVA, Harman, Heatplus, isobar, ivygapSE, les, lionessR, lumi, mammaPrintData, MAST, methylumi, MLP, msigdb, npGSEA, NxtIRFcore, oligo, oppar, piano, PREDA, proDA, puma, QFeatures, qsvaR, randRotation, recountmethylation, ribosomeProfilingQC, rtracklayer, seventyGeneData, signifinder, simpleSingleCell, spatialHeatmap, SpliceWiz, stageR, subSeq, SummarizedBenchmark, systemPipeR, TCGAbiolinks, tidybulk, topconfects, trena, tximeta, tximport, ViSEAGO, zFPKM |
| Links To Me |
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| Build Report |
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