To install this package, start R and enter:

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

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

limma

 

   

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

Linear Models for Microarray Data

Bioconductor version: Development (3.4)

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 wehi.edu.au>

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

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("limma")

 

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

Details

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 3.29.14
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 11 years)
License GPL (>=2)
Depends R (>= 2.3.0)
Imports grDevices, graphics, stats, utils, methods
LinkingTo
Suggests affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db, illuminaio, locfit, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn
SystemRequirements
Enhances
URL http://bioinf.wehi.edu.au/limma
Depends On Me a4Base, AffyExpress, AgiMicroRna, birta, bsseq, CALIB, CCl4, cghMCR, ChimpHumanBrainData, clippda, codelink, convert, Cormotif, coRNAi, DrugVsDisease, edgeR, ExiMiR, ExpressionAtlas, FEM, Fletcher2013a, gCMAP, genefu, HD2013SGI, HTqPCR, maigesPack, maPredictDSC, marray, metagenomeSeq, metaseqR, MLSeq, MmPalateMiRNA, NetCRG, PGPC, prot2D, qpcrNorm, qusage, RBM, Ringo, RnBeads, Rnits, snapCGH, splineTimeR, SSPA, tRanslatome, TurboNorm, wateRmelon
Imports Me ABSSeq, affycoretools, affylmGUI, ArrayExpress, arrayQuality, arrayQualityMetrics, ArrayTools, attract, ballgown, BatchQC, beadarray, BeadArrayUseCases, betr, birte, BubbleTree, bumphunter, CALIB, CancerMutationAnalysis, casper, ChAMP, charm, ChIPComp, ChIPpeakAnno, compcodeR, CONFESS, CountClust, crlmm, crossmeta, csaw, DAPAR, derfinderPlot, DiffBind, diffHic, DmelSGI, DMRcate, EBSEA, EGAD, EGSEA, erccdashboard, explorase, flowBin, GeneSelectMMD, GeneSelector, GGBase, GOsummaries, gQTLstats, HTqPCR, iCheck, iChip, iCOBRA, InPAS, limmaGUI, Linnorm, lmdme, LVSmiRNA, mAPKL, maSigPro, MEAL, minfi, miRLAB, missMethyl, MmPalateMiRNA, monocle, MSstats, nem, nethet, nondetects, OGSA, OLIN, PAA, PADOG, pbcmc, pcaExplorer, PECA, pepStat, phenoTest, polyester, qsea, rCGH, ReportingTools, Ringo, RNAinteract, RNAither, RTCGAToolbox, RTN, RTopper, scater, scran, sigaR, SimBindProfiles, snapCGH, STATegRa, systemPipeR, TCGAbiolinks, timecourse, ToPASeq, tweeDEseq, variancePartition, vsn
Suggests Me ABarray, ADaCGH2, beadarraySNP, biobroom, BiocCaseStudies, BioNet, Category, categoryCompare, ClassifyR, CMA, coGPS, derfinder, dyebias, ELBOW, gage, GeneSelector, GEOquery, GeuvadisTranscriptExpr, Glimma, GSRI, GSVA, Harman, Heatplus, isobar, les, lumi, mammaPrintData, mdgsa, methylumi, MLP, npGSEA, oligo, oneChannelGUI, oppar, paxtoolsr, PGSEA, piano, plw, PREDA, puma, Rcade, RTopper, rtracklayer, seventyGeneData, subSeq, sva, tximport
Build Report  

Package Archives

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

Package Source limma_3.29.14.tar.gz
Windows Binary limma_3.29.6.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) limma_3.29.14.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/limma
Package Short Url http://bioconductor.org/packages/limma/
Package Downloads Report Download Stats

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