limma

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

Linear Models for Microarray Data

Installation

To install this package, start R (version "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

A brief introduction to limma	HTML	R Script
limma User's Guide	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	3.57.7
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 18 years)
License	GPL (>=2)
Depends	R (>= 3.6.0)
Imports	grDevices, graphics, stats, utils, methods, statmod
Linking To
Suggests	BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines, affy, AnnotationDbi, Biobase, BiocStyle, GO.db, illuminaio, org.Hs.eg.db, vsn
System Requirements
Enhances
URL	https://bioinf.wehi.edu.au/limma/

See More

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, 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, 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, oligo, oppar, piano, PREDA, proDA, puma, QFeatures, qsvaR, randRotation, recountmethylation, ribosomeProfilingQC, rtracklayer, seventyGeneData, signifinder, simpleSingleCell, spatialHeatmap, SpliceWiz, stageR, subSeq, SummarizedBenchmark, systemPipeR, TCGAbiolinks, tidybulk, topconfects, tximeta, tximport, ViSEAGO, zFPKM
Links To Me
Build Report

Package Archives

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

Source Package	limma_3.57.7.tar.gz
Windows Binary	limma_3.57.7.zip
macOS Binary (x86_64)	limma_3.57.7.tgz
macOS Binary (arm64)	limma_3.57.7.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