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limma

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

Linear Models for Microarray Data


Bioconductor version: Development (3.19)

Data analysis, linear models and differential expression for microarray and RNA-seq 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], Goknur Giner [ctb], Mette Langaas [ctb], Egil Ferkingstad [ctb], Marcus Davy [ctb], Francois Pepin [ctb], Dongseok Choi [ctb], Charity Law [ctb], Mengbo Li [ctb]

Maintainer: Gordon Smyth <smyth at wehi.edu.au>

Citation (from within R, enter citation("limma")):

Installation

To install this package, start R (version "4.4") 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 3.59.9
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, statmod
System Requirements
URL https://bioinf.wehi.edu.au/limma/
See More
Suggests BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines, affy, AnnotationDbi, Biobase, BiocStyle, GO.db, illuminaio, org.Hs.eg.db, vsn
Linking To
Enhances
Depends On Me AgiMicroRna, ASpli, BLMA, CCl4, cghMCR, ChimpHumanBrainData, clippda, codelink, convert, Cormotif, 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, 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, BERT, 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, dreamlet, DRIMSeq, eegc, EGAD, EGSEA, eisaR, EnrichmentBrowser, epigraHMM, EpiMix, erccdashboard, EventPointer, EWCE, ExpHunterSuite, ExploreModelMatrix, ExpressionNormalizationWorkflow, flowBin, gCrisprTools, GDCRNATools, genefu, GeneSelectMMD, GEOquery, gg4way, Glimma, GRaNIE, GUIDEseq, GWAS.BAYES, HarmonizR, hermes, HERON, hipathia, HTqPCR, icetea, iCheck, iChip, iCOBRA, ideal, InPAS, isomiRs, KnowSeq, lemur, limmaGUI, Linnorm, lipidr, lmdme, mastR, MatrixQCvis, MBECS, MBQN, mCSEA, MEAL, methylKit, MethylMix, microbiomeExplorer, microbiomeMarker, miloR, minfi, MIRit, 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, qmtools, qPLEXanalyzer, qsea, rCGH, recountWorkflow, RegEnrich, regsplice, ReportingTools, RNAinteract, RNAseqCovarImpute, roastgsa, ROSeq, RTN, RTopper, saseR, satuRn, scClassify, scone, scran, ScreenR, scviR, seqsetvis, shinyepico, signatureSearchData, SimBindProfiles, SingleCellSignalR, singleCellTK, 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, Biobase, biobroom, BiocSet, BioNet, BioQC, BloodCancerMultiOmics2017, CAGEWorkflow, Category, categoryCompare, celaref, CellBench, CellMixS, ChIPpeakAnno, ClassifyR, CMA, coGPS, CONSTANd, cydar, Damsel, DAPAR, dar, dearseq, DEGreport, derfinder, DEScan2, dyebias, easyreporting, EnMCB, extraChIPs, fgsea, fishpond, fluentGenomics, gage, GeoTcgaData, GeuvadisTranscriptExpr, geva, glmGamPoi, GSRI, GSVA, Harman, Heatplus, iSEEde, isobar, ivygapSE, les, lionessR, lumi, lute, mammaPrintData, MAST, methylumi, MLP, msigdb, npGSEA, oligo, oppar, piano, PREDA, proDA, puma, QFeatures, qsvaR, raer, randRotation, recountmethylation, ribosomeProfilingQC, rtracklayer, Rvisdiff, seventyGeneData, signifinder, simpleSingleCell, spatialHeatmap, SpliceWiz, stageR, subSeq, SummarizedBenchmark, systemPipeR, tadar, 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_3.59.9.tar.gz
Windows Binary limma_3.59.9.zip
macOS Binary (x86_64) limma_3.59.9.tgz
macOS Binary (arm64) limma_3.59.9.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