limma

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see limma.

Linear Models for Microarray Data

Bioconductor version: 3.9

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 (version "3.6") 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

Need some help? Ask on the Bioconductor Support site!

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	3.40.6
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

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	a4Base, AffyExpress, AgiMicroRna, birta, BLMA, CALIB, CCl4, cghMCR, ChimpHumanBrainData, clippda, codelink, convert, Cormotif, deco, DEqMS, DrugVsDisease, edgeR, EGSEA123, ExiMiR, ExpressionAtlas, FEM, Fletcher2013a, gCMAP, genefu, HD2013SGI, HTqPCR, IsoformSwitchAnalyzeR, maEndToEnd, maigesPack, maPredictDSC, marray, metagenomeSeq, metaseqR, methylationArrayAnalysis, MmPalateMiRNA, mpra, PGPC, qpcrNorm, qusage, RBM, Ringo, RNAseq123, RnBeads, Rnits, snapCGH, splineTimeR, SRGnet, SSPA, tRanslatome, TurboNorm, variancePartition, wateRmelon
Imports Me	ABSSeq, affycoretools, affylmGUI, AMARETTO, anamiR, animalcules, anota2seq, ArrayExpress, arrayQuality, arrayQualityMetrics, ArrayTools, artMS, ATACseqQC, attract, ballgown, BatchQC, beadarray, BeadArrayUseCases, biotmle, birte, bsseq, BubbleTree, bumphunter, CALIB, CancerMutationAnalysis, CancerSubtypes, casper, CATALYST, CEMiTool, ChAMP, charm, ChIPComp, ChIPpeakAnno, clusterExperiment, CNVRanger, coexnet, compcodeR, CONFESS, consensusDE, consensusOV, CountClust, crlmm, crossmeta, csaw, cTRAP, ctsGE, DaMiRseq, DAPAR, debrowser, DEP, derfinderPlot, DEsubs, DiffBind, diffcyt, diffHic, diffloop, DmelSGI, DMRcate, Doscheda, DRIMSeq, EBSEA, eegc, EGAD, EGSEA, EnrichmentBrowser, erccdashboard, EventPointer, explorase, ExpressionNormalizationWorkflow, flowBin, gCrisprTools, GDCRNATools, GeneSelectMMD, GEOquery, GGBase, GOsummaries, gQTLstats, GUIDEseq, hipathia, HTqPCR, icetea, iCheck, iChip, iCOBRA, ideal, InPAS, isomiRs, limmaGUI, Linnorm, lipidr, lmdme, LVSmiRNA, mAPKL, mCSEA, MEAL, methylKit, MethylMix, methyvim, MIGSA, minfi, miRLAB, missMethyl, MLSeq, MmPalateMiRNA, monocle, MoonlightR, MSstats, MSstatsTMT, MultiDataSet, NADfinder, nem, nethet, nondetects, NormalyzerDE, OGSA, OLIN, omicRexposome, OVESEG, PAA, PADOG, PathoStat, pcaExplorer, PECA, pepStat, phantasus, phenoTest, polyester, projectR, psichomics, qPLEXanalyzer, qsea, rCGH, recountWorkflow, regsplice, ReportingTools, Ringo, RNAinteract, RNAither, RTCGAToolbox, RTN, RTopper, scone, scran, SEPIRA, seqsetvis, sigaR, SimBindProfiles, singleCellTK, snapCGH, STATegRa, sva, SVAPLSseq, systemPipeR, TCGAbiolinks, timecourse, TimeSeriesExperiment, ToPASeq, TPP, transcriptogramer, TVTB, tweeDEseq, vsn, Wrench, yamss, yarn
Suggests Me	ABarray, ADaCGH2, arrays, beadarraySNP, biobroom, BiocCaseStudies, BioNet, BloodCancerMultiOmics2017, CAGEWorkflow, Category, categoryCompare, celaref, CellBench, CellMixS, ClassifyR, CMA, coGPS, cydar, DEGreport, derfinder, DEScan2, dyebias, ELBOW, fgsea, gage, GeuvadisTranscriptExpr, Glimma, GSRI, GSVA, Harman, Heatplus, isobar, ivygapSE, les, lumi, mammaPrintData, MAST, mdgsa, methylumi, MLP, npGSEA, oligo, oppar, paxtoolsr, PGSEA, piano, plw, PREDA, puma, Rcade, RTopper, rtracklayer, scater, seventyGeneData, simpleSingleCell, stageR, subSeq, SummarizedBenchmark, topconfects, tximport, zFPKM
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	limma_3.40.6.tar.gz
Windows Binary	limma_3.40.6.zip
Mac OS X 10.11 (El Capitan)	limma_3.40.6.tgz
Source Repository	git clone https://git.bioconductor.org/packages/limma
Source Repository (Developer Access)	git clone [email protected]: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 3.9	Source Archive