limma

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see limma.

Linear Models for Microarray Data


Bioconductor version: 3.10

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

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 3.42.2
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 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, qpcrNorm, qusage, RBM, ReactomeGSA.data, Ringo, RNAseq123, RnBeads, Rnits, splineTimeR, SRGnet, SSPA, tRanslatome, TurboNorm, variancePartition, wateRmelon
Imports Me ABSSeq, affycoretools, affylmGUI, AMARETTO, anamiR, animalcules, anota2seq, ArrayExpress, arrayQuality, arrayQualityMetrics, ArrayTools, artMS, ASpediaFI, ATACseqQC, attract, AWFisher, ballgown, BatchQC, beadarray, BeadArrayUseCases, biotmle, birte, bsseq, BubbleTree, bumphunter, CALIB, CancerMutationAnalysis, CancerSubtypes, casper, CATALYST, ChAMP, ChIPComp, ChIPpeakAnno, clusterExperiment, CNVRanger, coexnet, compcodeR, CONFESS, consensusDE, consensusOV, CountClust, crlmm, CrossICC, 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, flowSpy, gCrisprTools, GDCRNATools, GeneSelectMMD, GEOquery, GGBase, GOsummaries, gQTLstats, GUIDEseq, hipathia, HTqPCR, icetea, iCheck, iChip, iCOBRA, ideal, InPAS, isomiRs, KnowSeq, limmaGUI, Linnorm, lipidr, lmdme, LVSmiRNA, mAPKL, MBQN, mCSEA, MEAL, methylKit, MethylMix, methyvim, MIGSA, minfi, miRLAB, missMethyl, MLSeq, MmPalateMiRNA, monocle, MoonlightR, MSstats, MSstatsTMT, MultiDataSet, muscat, NADfinder, nem, nethet, nondetects, NormalyzerDE, OGSA, OLIN, omicRexposome, oppti, OVESEG, PAA, PADOG, PathoStat, pcaExplorer, PECA, pepStat, phantasus, phenoTest, polyester, projectR, psichomics, pwrEWAS, qPLEXanalyzer, qsea, rCGH, recountWorkflow, regsplice, ReportingTools, Ringo, RNAinteract, RNAither, RTCGAToolbox, RTN, RTopper, scone, scran, SEPIRA, seqsetvis, sigaR, signatureSearchData, 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, BiocSet, 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, lionessR, lumi, mammaPrintData, MAST, mdgsa, methylumi, MLP, npGSEA, oligo, oppar, paxtoolsr, PGSEA, piano, plw, PREDA, proDA, puma, Rcade, RTopper, rtracklayer, scater, seventyGeneData, simpleSingleCell, stageR, subSeq, SummarizedBenchmark, 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_3.42.2.tar.gz
Windows Binary limma_3.42.2.zip
Mac OS X 10.11 (El Capitan) limma_3.42.2.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 3.10 Source Archive