limma

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see limma.

Linear Models for Microarray Data

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("limma")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("limma")

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

Details

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	3.48.3
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 19 years)
License	GPL (>=2)
Depends	R (>= 3.6.0)
Imports	grDevices, graphics, stats, utils, methods
System Requirements
URL	http://bioinf.wehi.edu.au/limma

See More

Suggests	affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db, gplots, illuminaio, locfit, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn
Linking To
Enhances
Depends On Me	AffyExpress, AgiMicroRna, ASpli, BLMA, CCl4, cghMCR, ChimpHumanBrainData, clippda, codelink, convert, Cormotif, deco, DEqMS, DrugVsDisease, edgeR, EGSEA123, ExiMiR, ExpressionAtlas, Fletcher2013a, HD2013SGI, HTqPCR, IsoformSwitchAnalyzeR, maEndToEnd, maigesPack, maPredictDSC, marray, metagenomeSeq, metaseqR2, methylationArrayAnalysis, mpra, qpcrNorm, qusage, RBM, ReactomeGSA.data, Ringo, RNAseq123, RnBeads, Rnits, splineTimeR, SRGnet, TOAST, tRanslatome, TurboNorm, variancePartition, wateRmelon
Imports Me	a4Base, ABSSeq, affycoretools, affylmGUI, AMARETTO, animalcules, anota2seq, ArrayExpress, arrayQuality, arrayQualityMetrics, ArrayTools, artMS, ASpediaFI, ATACseqQC, attract, autonomics, AWFisher, ballgown, BatchQC, beadarray, BeadArrayUseCases, biotmle, BloodGen3Module, bnem, bsseq, BubbleTree, bumphunter, CancerMutationAnalysis, CancerSubtypes, casper, ChAMP, ChIPComp, clusterExperiment, CNVRanger, coexnet, combi, compcodeR, CONFESS, consensusDE, consensusOV, CountClust, crlmm, CrossICC, crossmeta, csaw, cTRAP, ctsGE, CytoTree, DAMEfinder, DaMiRseq, DAPAR, debrowser, DEP, derfinderPlot, DEsubs, DExMA, DiffBind, diffcyt, diffHic, diffloop, diffUTR, distinct, DmelSGI, DMRcate, Doscheda, DRIMSeq, eegc, EGAD, EGSEA, eisaR, EnrichmentBrowser, epigraHMM, erccdashboard, escape, EventPointer, EWCE, ExpHunterSuite, ExploreModelMatrix, ExpressionNormalizationWorkflow, flowBin, gCrisprTools, GDCRNATools, genefu, GeneSelectMMD, GEOquery, Glimma, GOsummaries, GUIDEseq, hipathia, HTqPCR, icetea, iCheck, iChip, iCOBRA, ideal, InPAS, isomiRs, KnowSeq, limmaGUI, Linnorm, lipidr, lmdme, mAPKL, MatrixQCvis, MBQN, mCSEA, MEAL, methylKit, MethylMix, microbiomeExplorer, MIGSA, miloR, minfi, miRLAB, missMethyl, MLSeq, moanin, monocle, MoonlightR, msImpute, msqrob2, MSstats, MSstatsTMT, MultiDataSet, muscat, NADfinder, nethet, nondetects, NormalyzerDE, OLIN, omicRexposome, oppti, OVESEG, PAA, PADOG, PathoStat, pcaExplorer, PECA, pepStat, phantasus, phenoTest, PhosR, polyester, POMA, POWSC, projectR, psichomics, pwrEWAS, qPLEXanalyzer, qsea, rCGH, recountWorkflow, RegEnrich, regsplice, ReportingTools, Ringo, RNAinteract, RNAither, ROSeq, RTCGAToolbox, RTN, RTopper, satuRn, scClassify, scone, scran, SEPIRA, seqsetvis, shinyepico, signatureSearchData, SimBindProfiles, SingleCellSignalR, singleCellTK, snapCGH, SPsimSeq, SSPA, STATegRa, sva, systemPipeR, timecourse, TimeSeriesExperiment, ToPASeq, ToxicoGx, TPP, TPP2D, transcriptogramer, TVTB, tweeDEseq, vsn, weitrix, Wrench, yamss, yarn
Suggests Me	ABarray, ADaCGH2, arrays, beadarraySNP, biobroom, BiocCaseStudies, BiocSet, BioNet, BioQC, BloodCancerMultiOmics2017, CAGEWorkflow, Category, categoryCompare, celaref, CellBench, CellMixS, ChIPpeakAnno, ClassifyR, CMA, coGPS, CONSTANd, cydar, dearseq, DEGreport, derfinder, DEScan2, dyebias, easyreporting, ELBOW, fgsea, fishpond, fluentGenomics, gage, GeuvadisTranscriptExpr, geva, glmGamPoi, GSRI, GSVA, Harman, Heatplus, isobar, ivygapSE, les, lionessR, lumi, mammaPrintData, MAST, mdgsa, methylumi, MLP, msigdb, npGSEA, oligo, oppar, piano, PREDA, proDA, puma, QFeatures, randRotation, Rcade, recountmethylation, ribosomeProfilingQC, rtracklayer, seventyGeneData, simpleSingleCell, stageR, subSeq, SummarizedBenchmark, TCGAbiolinks, tidybulk, topconfects, tximeta, tximport, ViSEAGO, zFPKM
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	limma_3.48.3.tar.gz
Windows Binary	limma_3.48.3.zip
macOS 10.13 (High Sierra)	limma_3.48.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/limma
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/limma
Bioc Package Browser	https://code.bioconductor.org/browse/limma/
Package Short Url	https://bioconductor.org/packages/limma/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.13	Source Archive