limma

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

Linear Models for Microarray and Omics Data

Bioconductor version: Development (3.24)

Data analysis, linear models and differential expression for omics data.

Author: Gordon Smyth [cre, aut] ORCID: 0000-0001-9221-2892 , Lizhong Chen [aut] ORCID: 0000-0002-8326-6781 , Matthew Ritchie [ctb], Belinda Phipson [ctb], Di Wu [ctb], Yifang Hu [ctb], Charity Law [ctb], Wei Shi [ctb], James Wettenhall [ctb], Yunshun Chen [ctb], Mengbo Li [ctb], Jeremy Silver [ctb], Aaron Lun [ctb], Davis McCarthy [ctb], Natalie Thorne [ctb], Carolyn de Graaf [ctb], Goknur Giner [ctb], Alicia Oshlack [ctb], Marcus Davy [ctb], Mette Langaas [ctb], Egil Ferkingstad [ctb], Francois Pepin [ctb], Dongseok Choi [ctb]

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

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

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

Installation

To install this package, start R (version "4.6") and enter:


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

## The following initializes the development version of Bioconductor
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

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	3.99.2
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 21.5 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/

Suggests	BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines, affy, AnnotationDbi, Biobase, BiocStyle, GO.db, illuminaio, org.Hs.eg.db, SummarizedExperiment, vsn
Linking To
Enhances
Depends On Me	ASpli, BLMA, cghMCR, codelink, convert, Cormotif, DrugVsDisease, edgeR, ExiMiR, ExpressionAtlas, HTqPCR, IsoformSwitchAnalyzeR, limpa, marray, metagenomeSeq, metaseqR2, mpra, NanoTube, octad, protGear, qpcrNorm, qusage, RBM, RnBeads, Rnits, splineTimeR, TMSig, TOAST, tRanslatome, TurboNorm, variancePartition, wateRmelon, zenith, CCl4, Fletcher2013a, HD2013SGI, ReactomeGSA.data, EGSEA123, methylationArrayAnalysis, RNAseq123, OSCA.advanced, OSCA.basic, OSCA.workflows, BALLI, BioInsight, CEDA, cp4p, DAAGbio, DRomics, fmt, PerfMeas
Imports Me	a4Base, ABSSeq, affycoretools, affylmGUI, AMARETTO, animalcules, ArrayExpress, arrayQuality, arrayQualityMetrics, artMS, ATACseqQC, ATACseqTFEA, attract, autonomics, AWFisher, ballgown, barbieQ, BatChef, BatchQC, beadarray, benchdamic, BERT, biotmle, BloodGen3Module, bnem, bsseq, bumphunter, casper, ChAMP, CleanUpRNAseq, clusterExperiment, CNVRanger, combi, compcodeR, consensusOV, crlmm, csaw, cTRAP, ctsGE, DAMEfinder, damidBind, DaMiRseq, debrowser, DeeDeeExperiment, DELocal, derfinderPlot, DESpace, DEsubs, DExMA, DiffBind, diffcyt, diffHic, diffUTR, distinct, DMRcate, Doscheda, dreamlet, DRIMSeq, DspikeIn, EGAD, EGSEA, eisaR, EnrichmentBrowser, epigraHMM, EpiMix, erccdashboard, EventPointer, EWCE, ExploreModelMatrix, flowBin, gCrisprTools, GDCRNATools, genefu, GeneSelectMMD, GEOquery, gg4way, gINTomics, Glimma, GRaNIE, GWAS.BAYES, HarmonizR, hermes, HERON, hipathia, HTqPCR, icetea, iCheck, iChip, iCOBRA, ideal, InPAS, isomiRs, KnowSeq, lemur, limmaGUI, LimROTS, Linnorm, lipidr, lmdme, markeR, mastR, MatrixQCvis, MBECS, MBQN, mCSEA, MEAL, MetaProViz, methylKit, MethylMix, microbiomeExplorer, miloR, minfi, MIRit, miRLAB, missMethyl, MLSeq, moanin, monocle, MoonlightR, msImpute, mspms, msqrob2, MSstats, MSstatsTMT, MultiDataSet, muscat, mutscan, NADfinder, NanoMethViz, nethet, nondetects, NormalyzerDE, notameViz, OLIN, omicRexposome, OVESEG, PAA, PADOG, pairedGSEA, PanomiR, PathoStat, pcaExplorer, PECA, PepSetTest, pepStat, phantasus, phenoTest, PhosR, PolySTest, POMA, POWSC, proBatch, projectR, PRONE, psichomics, qmtools, qPLEXanalyzer, qsea, RegEnrich, regsplice, RFGeneRank, RFLOMICS, RNAseqCovarImpute, roastgsa, ROSeq, RTN, RTopper, saseR, satuRn, scClassify, scone, scQTLtools, scran, ScreenR, scviR, seqsetvis, shinyDSP, shinyepico, singleCellTK, SmartPhos, sparrow, speckle, SpNeigh, SPsimSeq, standR, STATegRa, Statial, structToolbox, sva, tidyexposomics, timecourse, TOP, ToxicoGx, TPP, TPP2D, transcriptogramer, TVTB, tweeDEseq, unifiedWMWqPCR, VISTA, vsclust, vsn, weitrix, Wrench, XAItest, yamss, yarn, BeadArrayUseCases, signatureSearchData, spatialLIBD, ExpHunterSuite, ExpressionNormalizationWorkflow, recountWorkflow, batchtma, BPM, Cascade, cinaR, diffwrap, DiPALM, dsb, eLNNpairedCov, GSEMA, hicream, lfproQC, lilikoi, limorhyde2, lipidomeR, MetAlyzer, metaMA, mi4p, miRtest, MKmisc, MKomics, MSclassifR, newIMVC, nlcv, oncoPredict, OncoSubtype, Patterns, plfMA, promor, RANKS, RCPA, robusttseq, RPPanalyzer, scBio, scGOclust, scROSHI, ssizeRNA, tinyarray, TransProR, treediff, wrProteo, XYomics
Suggests Me	ABarray, ADaCGH2, Biobase, biobroom, BiocSet, BioNet, BioQC, blase, broadSeq, Category, categoryCompare, celaref, CellBench, CellMixS, ChIPpeakAnno, ClassifyR, CMA, coGPS, CONSTANd, cydar, Damsel, DAPAR, dar, dearseq, DEGreport, derfinder, DEScan2, dyebias, easyreporting, EnMCB, extraChIPs, fgsea, fishpond, gage, GeoTcgaData, geva, glmGamPoi, GSRI, GSVA, Harman, Heatplus, iSEEde, isobar, ivygapSE, les, lumi, MAST, methylumi, MLP, npGSEA, oligo, oppar, piano, PREDA, proDA, puma, QFeatures, qsvaR, raer, randRotation, recountmethylation, ribosomeProfilingQC, rtracklayer, Rvisdiff, scFeatures, signifinder, spatialHeatmap, SpliceWiz, stageR, subSeq, systemPipeR, tadar, TCGAbiolinks, TFEA.ChIP, tidybulk, topconfects, tximeta, tximport, ViSEAGO, zFPKM, BloodCancerMultiOmics2017, bugphyzz, GeuvadisTranscriptExpr, mammaPrintData, msigdb, seventyGeneData, arrays, CAGEWorkflow, fluentGenomics, simpleSingleCell, AnnoProbe, aroma.affymetrix, canvasXpress, corncob, DGEobj.utils, easybio, ggpicrust2, GiANT, hexbin, inDAGO, IOBR, limorhyde, maGUI, MosaiClusteR, NACHO, pctax, pmartR, protti, RepeatedHighDim, seqgendiff, Seurat, SeuratExplorer, simphony, st, volcano3D, wrGraph, wrMisc
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	limma_3.99.2.tar.gz
Windows Binary (x86_64)	limma_3.99.2.zip (64-bit only)
macOS Binary (big-sur-x86_64)	limma_3.99.2.tgz
macOS Binary (sonoma-arm64)	limma_3.99.2.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