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

Linear Models for Microarray Data

Bioconductor version: Development (3.5)

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]

Maintainer: Gordon Smyth <smyth at>

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PDF Limma One Page Introduction
PDF usersguide.pdf
PDF   Reference Manual
Text   NEWS


biocViews AlternativeSplicing, BatchEffect, Bayesian, Clustering, DataImport, DifferentialExpression, DifferentialSplicing, ExonArray, GeneExpression, GeneSetEnrichment, Genetics, Microarray, MultipleComparison, Normalization, OneChannel, Preprocessing, ProprietaryPlatforms, QualityControl, RNASeq, Regression, Software, TimeCourse, Transcription, TwoChannel, mRNAMicroarray, microRNAArray
Version 3.31.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 11.5 years)
License GPL (>=2)
Depends R (>= 2.3.0)
Imports grDevices, graphics, stats, utils, methods
Suggests affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db, illuminaio, locfit, MASS,, splines, statmod (>= 1.2.2), vsn
Depends On Me a4Base, AffyExpress, AgiMicroRna, birta, bsseq, CALIB, cghMCR, clippda, codelink, convert, Cormotif, coRNAi, DrugVsDisease, edgeR, ExiMiR, ExpressionAtlas, FEM, gCMAP, genefu, HTqPCR, maigesPack, maPredictDSC, marray, metagenomeSeq, metaseqR, MLSeq, MmPalateMiRNA, prot2D, qpcrNorm, qusage, RBM, Ringo, RnBeads, Rnits, snapCGH, splineTimeR, SRGnet, SSPA, tRanslatome, TurboNorm, wateRmelon
Imports Me ABSSeq, affycoretools, affylmGUI, anamiR, ArrayExpress, arrayQuality, arrayQualityMetrics, ArrayTools, attract, ballgown, BatchQC, beadarray, birte, BubbleTree, bumphunter, CALIB, CancerMutationAnalysis, CancerSubtypes, casper, ChAMP, charm, ChIPComp, ChIPpeakAnno, clusterExperiment, compcodeR, CONFESS, CountClust, crlmm, crossmeta, csaw, ctsGE, DAPAR, debrowser, derfinderPlot, DEsubs, DiffBind, diffHic, DMRcate, EBSEA, eegc, EGAD, EGSEA, EnrichmentBrowser, erccdashboard, explorase, flowBin, gCrisprTools, GeneSelectMMD, GeneSelector, GGBase, GOsummaries, gQTLstats, GUIDEseq, HTqPCR, iCheck, iChip, iCOBRA, InPAS, limmaGUI, Linnorm, lmdme, LVSmiRNA, mAPKL, MEAL, methylKit, minfi, miRLAB, missMethyl, MmPalateMiRNA, monocle, MoonlightR, MSstats, nem, nethet, nondetects, OGSA, OLIN, PAA, PADOG, PathoStat, pbcmc, pcaExplorer, PECA, pepStat, polyester, qsea, rCGH, regsplice, ReportingTools, Ringo, RNAinteract, RNAither, RTCGAToolbox, RTN, RTopper, scater, sigaR, SimBindProfiles, snapCGH, STATegRa, SVAPLSseq, systemPipeR, TCGAbiolinks, timecourse, ToPASeq, TPP, tweeDEseq, variancePartition, vsn, yamss, yarn
Suggests Me ABarray, ADaCGH2, beadarraySNP, biobroom, BiocCaseStudies, BioNet, Category, categoryCompare, ClassifyR, CMA, coGPS, derfinder, dyebias, ELBOW, gage, GeneSelector, GEOquery, Glimma, GSRI, GSVA, Harman, Heatplus, isobar, les, MAST, mdgsa, methylumi, MLP, npGSEA, oligo, oneChannelGUI, oppar, paxtoolsr, PGSEA, piano, plw, PREDA, puma, Rcade, RTopper, rtracklayer, scran, subSeq, sva, tximport
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