limma

DOI: 10.18129/B9.bioc.limma    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see limma.

Linear Models for Microarray Data

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

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

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	3.38.3
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 14 years)
License	GPL (>=2)
Depends	R (>= 2.3.0)
Imports	grDevices, graphics, stats, utils, methods
LinkingTo
Suggests	affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db, gplots, 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, BLMA, CALIB, CCl4, cghMCR, ChimpHumanBrainData, clippda, codelink, convert, Cormotif, DEqMS, DrugVsDisease, edgeR, EGSEA123, ExiMiR, ExpressionAtlas, FEM, Fletcher2013a, gCMAP, genefu, HD2013SGI, HTqPCR, IsoformSwitchAnalyzeR, maEndToEnd, maigesPack, maPredictDSC, marray, metagenomeSeq, metaseqR, methylationArrayAnalysis, MmPalateMiRNA, mpra, PGPC, prot2D, qpcrNorm, qusage, RBM, Ringo, RNAseq123, RnBeads, Rnits, simpleSingleCell, snapCGH, splineTimeR, SRGnet, SSPA, tRanslatome, TurboNorm, variancePartition, wateRmelon
Imports Me	ABSSeq, affycoretools, affylmGUI, anamiR, 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, coexnet, compcodeR, CONFESS, consensusDE, consensusOV, CountClust, crlmm, crossmeta, csaw, cTRAP, ctsGE, cytofWorkflow, 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, GeneSelector, GEOquery, GGBase, GOsummaries, gQTLstats, GUIDEseq, hipathia, HTqPCR, icetea, iCheck, iChip, iCOBRA, ideal, InPAS, IsoformSwitchAnalyzeR, isomiRs, limmaGUI, Linnorm, 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, PAA, PADOG, PathoStat, pbcmc, pcaExplorer, PECA, pepStat, phantasus, phenoTest, polyester, 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, TPP, transcriptogramer, TVTB, tweeDEseq, vsn, Wrench, yamss, yarn
Suggests Me	ABarray, ADaCGH2, arrays, beadarraySNP, biobroom, BiocCaseStudies, BioNet, BloodCancerMultiOmics2017, Category, categoryCompare, celaref, ClassifyR, CMA, coGPS, cydar, DEGreport, derfinder, DEScan2, dyebias, ELBOW, fgsea, gage, GeneSelector, 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, stageR, subSeq, SummarizedBenchmark, tximport, zFPKM
Links To Me
Build Report

Package Archives

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

Source Package	limma_3.38.3.tar.gz
Windows Binary	limma_3.38.3.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	limma_3.38.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/limma
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/limma
Package Short Url	http://bioconductor.org/packages/limma/
Package Downloads Report	Download Stats