limma

This is the released version of limma; for the devel version, see limma.

Linear Models for Microarray and Omics Data

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DOI: 10.18129/B9.bioc.limma

Bioconductor version: Release (3.22)

Data analysis, linear models and differential expression for omics 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], Lizhong Chen [ctb]

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

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

Installation

To install this package, start R (version "4.5") 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")

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

Version 3.66.0

In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 20.5 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, 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, maEndToEnd, 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, artMS, ATACseqQC, ATACseqTFEA, attract, autonomics, AWFisher, ballgown, barbieQ, BatchQC, BERT, biotmle, BloodGen3Module, bnem, bsseq, bumphunter, casper, ChAMP, CleanUpRNAseq, clusterExperiment, CNVRanger, combi, compcodeR, consensusDE, consensusOV, crlmm, csaw, cTRAP, ctsGE, DAMEfinder, DaMiRseq, debrowser, DeeDeeExperiment, DEP, 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, Glimma, GRaNIE, GWAS.BAYES, HarmonizR, hermes, HERON, HTqPCR, icetea, iCheck, iChip, iCOBRA, ideal, InPAS, KnowSeq, lemur, limmaGUI, LimROTS, Linnorm, lipidr, lmdme, markeR, mastR, MatrixQCvis, MBECS, MBQN, mCSEA, MEAL, 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, OLIN, omicRexposome, OVESEG, PAA, PADOG, pairedGSEA, PanomiR, PathoStat, pcaExplorer, PECA, PepSetTest, pepStat, phantasus, phenomis, phenoTest, PhosR, PolySTest, POMA, POWSC, projectR, PRONE, psichomics, qmtools, qPLEXanalyzer, qsea, RegEnrich, regsplice, RFLOMICS, RNAseqCovarImpute, roastgsa, ROSeq, RTN, RTopper, saseR, satuRn, scClassify, scone, scran, scviR, seqsetvis, shinyDSP, shinyepico, singleCellTK, SmartPhos, sparrow, speckle, SPsimSeq, standR, STATegRa, Statial, sva, timecourse, TOP, ToxicoGx, TPP, TPP2D, transcriptogramer, TVTB, tweeDEseq, unifiedWMWqPCR, vsclust, vsn, weitrix, Wrench, XAItest, yamss, yarn, BeadArrayUseCases, signatureSearchData, spatialLIBD, ExpHunterSuite, ExpressionNormalizationWorkflow, recountWorkflow, aliases2entrez, batchtma, BPM, Cascade, cinaR, DiPALM, dsb, eLNNpairedCov, Grouphmap, GSEMA, GWASbyCluster, hicream, lfproQC, lilikoi, limorhyde2, lipidomeR, MetAlyzer, metaMA, mi4p, miRtest, MKmisc, MKomics, MSclassifR, newIMVC, nlcv, OncoSubtype, Patterns, plfMA, promor, RANKS, RCPA, RPPanalyzer, scBio, scGOclust, scRNAtools, scROSHI, ssizeRNA, tinyarray, TransProR, treediff, wrProteo, XYomics

Suggests Me ABarray, ADaCGH2, Biobase, biobroom, BiocSet, BioNet, BioQC, blase, 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, signifinder, 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, limorhyde, maGUI, NACHO, pctax, Platypus, pmartR, protti, RepeatedHighDim, SCdeconR, seqgendiff, Seurat, 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_3.66.0.tar.gz

Windows Binary (x86_64) limma_3.66.0.zip

macOS Binary (x86_64) limma_3.66.0.tgz

macOS Binary (arm64) limma_3.66.0.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/

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