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limma

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

All versions 3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5

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 iD ORCID: 0000-0001-9221-2892 , Lizhong Chen [aut] ORCID iD ORCID: 0000-0002-8326-6781 , 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], Yunshun Chen [ctb], Mengbo Li [ctb], Natalie Thorne [ctb], Carolyn de Graaf [ctb], Goknur Giner [ctb], Charity Law [ctb], Alicia Oshlack [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")):

Gordon Smyth, Lizhong Chen. limma: Linear Models for Microarray and Omics Data. doi:10.18129/B9.bioc.limma, R package version 3.99.0, https://bioconductor.org/packages/limma.

Generated from the package metadata; it may differ from the package's own citation.

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")
limma User's Guide PDF
A brief introduction to limma HTML R Script
Reference ManualPDF
NEWSText
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
Version3.99.0
In Bioconductor sinceBioC 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
URLhttps://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, SummarizedExperiment, vsn
Linking To
Enhances
Depends On Me AgiMicroRna, ASpli, BALLI, BioInsight, BLMA, CCl4, CEDA, cghMCR, ChimpHumanBrainData, clippda, codelink, convert, Cormotif, cp4p, DAAGbio, DEqMS, DRomics, DrugVsDisease, edgeR, EGSEA123, ExiMiR, ExpressionAtlas, Fletcher2013a, fmt, HD2013SGI, HTqPCR, IsoformSwitchAnalyzeR, limpa, maEndToEnd, maPredictDSC, marray, metagenomeSeq, metaseqR2, methylationArrayAnalysis, mpra, NanoTube, octad, OSCA.advanced, OSCA.workflows, PerfMeas, protGear, qpcrNorm, qusage, RBM, ReactomeGSA.data, RNAseq123, RnBeads, Rnits, spammR, splineTimeR, TMSig, TOAST, tRanslatome, ttScreening, TurboNorm, variancePartition, wateRmelon, zenith
Imports Me a4Base, ABSSeq, affycoretools, affylmGUI, AMARETTO, animalcules, anota2seq, ArrayExpress, arrayQuality, arrayQualityMetrics, artMS, ATACseqQC, ATACseqTFEA, attract, augere.de, augere.gsea, augere.screen, autonomics, AWFisher, barbieQ, BatChef, BatchQC, batchtma, beadarray, BeadArrayUseCases, benchdamic, BERT, biotmle, BloodGen3Module, bnem, BPM, bsseq, bumphunter, Cascade, casper, ChAMP, cinaR, CleanUpRNAseq, clusterExperiment, CNVRanger, combi, compcodeR, CONFESS, consensusOV, crlmm, csaw, ctdR, cTRAP, ctsGE, DAMEfinder, damidBind, DaMiRseq, daVis, debrowser, DeeDeeExperiment, DELocal, DEP, derfinderPlot, DESpace, DEsubs, DExMA, DiffBind, diffcyt, diffHic, diffUTR, diffwrap, DiPALM, distinct, DMRcate, dnaEPICO, Doscheda, dreamlet, DRIMSeq, dsb, DspikeIn, EGAD, EGSEA, eisaR, eLNNpairedCov, EnrichmentBrowser, epigraHMM, EpiMix, erccdashboard, EventPointer, EWCE, ExpHunterSuite, ExploreModelMatrix, ExpressionNormalizationWorkflow, flowBin, gCrisprTools, GDCRNATools, genefu, GeneSelectMMD, GEOquery, GExPipe, gg4way, gINTomics, Glimma, GRaNIE, GSEAlens, GSEMA, GUIDEseq, GWAS.BAYES, GWASbyCluster, HarmonizR, hermes, HERON, hicream, hipathia, HTqPCR, icetea, iCheck, iChip, iCOBRA, ideal, InPAS, isomiRs, KnowSeq, lemur, lfproQC, lilikoi, limmaGUI, limorhyde2, LimROTS, Linnorm, LIPIDIFy, lipidomeR, lipidr, lmdme, markeR, mastR, MatrixQCvis, MBECS, MBQN, mCSEA, MEAL, MetAlyzer, metaMA, MetaProViz, methylKit, MethylMix, mi4p, microbiomeExplorer, miloR, minfi, MIRit, miRLAB, miRtest, missMethyl, MKmisc, MKomics, MLSeq, monocle, MoonlightR, MSclassifR, msImpute, mspms, msqrob2, MSstats, MSstatsTMT, MultiDataSet, MultiOmicsBridge, muscat, mutscan, NADfinder, NanoMethViz, nethet, netZooR, newIMVC, nlcv, nondetects, NormalyzerDE, notameViz, OLIN, omicRexposome, oncoPredict, OncoSubtype, OVESEG, PAA, PADOG, pairedGSEA, PanomiR, PathoStat, Patterns, pcaExplorer, PECA, PepSetTest, pepStat, phantasus, phenomis, phenoTest, PhosR, plfMA, PolySTest, POMA, POWSC, proBatch, projectR, promor, PRONE, ProteinBatcher, psichomics, qmtools, qPLEXanalyzer, qsea, RANKS, rCGH, RCPA, recountWorkflow, RegEnrich, regsplice, ReportingTools, RFGeneRank, RFLOMICS, RNAseqCovarImpute, roastgsa, robusttseq, ROSeq, RPPanalyzer, RTN, RTopper, saseR, satuRn, scBio, scClassify, scCompoundDE, scFastDE, scGOclust, scone, scQTLtools, scran, ScreenR, scROSHI, seqsetvis, shinyDSP, shinyepico, signatureSearchData, singleCellTK, SmartPhos, sparrow, spatialLIBD, speckle, SpNeigh, SPsimSeq, ssizeRNA, standR, STATegRa, Statial, structToolbox, sva, TiDEomics, tidyexposomics, timecourse, tinyarray, TOP, ToxicoGx, TPP, TPP2D, TraianProt, transcriptogramer, TransProR, treediff, TVTB, tweeDEseq, unifiedWMWqPCR, VISTA, vsclust, vsn, weitrix, Wrench, wrProteo, XAItest, XYomics, yamss, yarn
Suggests Me ABarray, ADaCGH2, AnnoProbe, aroma.affymetrix, arrays, augere.core, Biobase, BiocSet, BioNet, BioQC, blase, BloodCancerMultiOmics2017, broadSeq, bugphyzz, CAGEWorkflow, canvasXpress, Category, categoryCompare, celaref, CellBench, CellMixS, ChIPpeakAnno, ClassifyR, CMA, coGPS, CONSTANd, corncob, cydar, Damsel, DAPAR, DaparToolshed, dar, DAssemble, dearseq, DEGreport, derfinder, DEScan2, DGEobj.utils, dyebias, easybio, easyreporting, EnMCB, extraChIPs, fgsea, fishpond, fluentGenomics, gage, GeoTcgaData, GeuvadisTranscriptExpr, geva, ggpicrust2, GiANT, glmGamPoi, GSRI, GSVA, Harman, Heatplus, hexbin, inDAGO, IOBR, iSEEde, isobar, ivygapSE, les, levi, limorhyde, lionessR, lumi, maGUI, mammaPrintData, MAST, methylumi, MLP, MosaiClusteR, msigdb, NACHO, normScore, npGSEA, oligo, oppar, pctax, piano, pmartR, PREDA, proDA, protti, puma, QFeatures, qsvaR, raer, randRotation, recountmethylation, RepeatedHighDim, ribosomeProfilingQC, rtracklayer, Rvisdiff, scFeatures, seqgendiff, Seurat, SeuratExplorer, seventyGeneData, signifinder, simphony, simpleSingleCell, spatialHeatmap, SpliceWiz, st, stageR, subSeq, systemPipeR, tadar, TCGAbiolinks, TFEA.ChIP, tidybulk, topconfects, tximeta, tximport, ViSEAGO, volcano3D, wrGraph, wrMisc, zFPKM
Links To Me
Build Report Build Report, r-universe

Package Archives

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

Source Package limma_3.99.0.tar.gz
Windows Binary (x86_64) limma_3.99.0.zip (64-bit only)
macOS Binary (big-sur-x86_64) limma_3.99.0.tgz
macOS Binary (sonoma-arm64) limma_3.99.0.tgz
Source Repositorygit clone https://git.bioconductor.org/packages/limma
Source Repository (Developer Access)git clone git@git.bioconductor.org:packages/limma
Package Short Url https://bioconductor.org/packages/limma/
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