limma

DOI: 10.18129/B9.bioc.limma    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see limma.

Linear Models for Microarray Data

Bioconductor version: 3.11

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>

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

Installation

To install this package, start R (version "4.0") 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 3.44.3
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 15.5 years)
License GPL (>=2)
Depends R (>= 3.6.0)
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, deco, DEqMS, DrugVsDisease, edgeR, EGSEA123, ExiMiR, ExpressionAtlas, FEM, Fletcher2013a, gCMAP, genefu, HD2013SGI, HTqPCR, IsoformSwitchAnalyzeR, maEndToEnd, maigesPack, maPredictDSC, marray, metagenomeSeq, metaseqR, metaseqR2, methylationArrayAnalysis, MmPalateMiRNA, mpra, qpcrNorm, qusage, RBM, ReactomeGSA.data, Ringo, RNAseq123, RnBeads, Rnits, splineTimeR, SRGnet, TOAST, tRanslatome, TurboNorm, variancePartition, wateRmelon
Imports Me ABSSeq, affycoretools, affylmGUI, AMARETTO, anamiR, animalcules, anota2seq, ArrayExpress, arrayQuality, arrayQualityMetrics, ArrayTools, artMS, ASpediaFI, ATACseqQC, attract, AWFisher, ballgown, BatchQC, beadarray, BeadArrayUseCases, biotmle, bsseq, BubbleTree, bumphunter, CALIB, CancerMutationAnalysis, CancerSubtypes, casper, ChAMP, ChIPComp, ChIPpeakAnno, clusterExperiment, CNVRanger, coexnet, combi, compcodeR, CONFESS, consensusDE, consensusOV, CountClust, crlmm, CrossICC, crossmeta, csaw, cTRAP, ctsGE, DAMEfinder, DaMiRseq, DAPAR, debrowser, DEP, derfinderPlot, DEsubs, DiffBind, diffcyt, diffHic, diffloop, distinct, DmelSGI, DMRcate, Doscheda, DRIMSeq, EBSEA, eegc, EGAD, EGSEA, eisaR, EnrichmentBrowser, erccdashboard, EventPointer, explorase, ExploreModelMatrix, ExpressionNormalizationWorkflow, flowBin, flowSpy, gCrisprTools, GDCRNATools, GeneSelectMMD, GEOquery, GGBase, GOsummaries, gQTLstats, GUIDEseq, hipathia, HTqPCR, icetea, iCheck, iChip, iCOBRA, ideal, InPAS, isomiRs, KnowSeq, limmaGUI, Linnorm, lipidr, lmdme, LVSmiRNA, mAPKL, MBQN, mCSEA, MEAL, methylKit, MethylMix, methyvim, MIGSA, minfi, miRLAB, missMethyl, MLSeq, MmPalateMiRNA, monocle, MoonlightR, MSstats, MSstatsTMT, MultiDataSet, muscat, NADfinder, nem, nethet, nondetects, NormalyzerDE, OGSA, OLIN, omicRexposome, oppti, OVESEG, PAA, PADOG, PathoStat, pcaExplorer, PECA, pepStat, phantasus, phenoTest, polyester, projectR, psichomics, pwrEWAS, qPLEXanalyzer, qsea, rCGH, recountWorkflow, regsplice, ReportingTools, Ringo, RNAinteract, RNAither, ROSeq, RTCGAToolbox, RTN, RTopper, scClassify, scone, scran, SEPIRA, seqsetvis, sigaR, signatureSearchData, SimBindProfiles, SingleCellSignalR, singleCellTK, snapCGH, SSPA, STATegRa, sva, SVAPLSseq, systemPipeR, timecourse, TimeSeriesExperiment, ToPASeq, TPP, TPP2D, transcriptogramer, TVTB, tweeDEseq, vsn, weitrix, Wrench, yamss, yarn
Suggests Me ABarray, ADaCGH2, arrays, beadarraySNP, biobroom, BiocCaseStudies, BiocSet, BioNet, BloodCancerMultiOmics2017, CAGEWorkflow, Category, categoryCompare, celaref, CellBench, CellMixS, ClassifyR, CMA, coGPS, cydar, dearseq, DEGreport, derfinder, DEScan2, dyebias, easyreporting, ELBOW, fgsea, fluentGenomics, gage, GeuvadisTranscriptExpr, Glimma, GSRI, GSVA, Harman, Heatplus, isobar, ivygapSE, les, lionessR, lumi, mammaPrintData, MAST, mdgsa, methylumi, MLP, npGSEA, oligo, oppar, PGSEA, piano, plw, PREDA, proDA, puma, randRotation, Rcade, ribosomeProfilingQC, RTopper, rtracklayer, scater, seventyGeneData, simpleSingleCell, stageR, subSeq, SummarizedBenchmark, TCGAbiolinks, tidybulk, topconfects, tximeta, tximport, ViSEAGO, zFPKM
Links To Me
Build Report  

Package Archives

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

Source Package limma_3.44.3.tar.gz
Windows Binary limma_3.44.3.zip (32- & 64-bit)
macOS 10.13 (High Sierra) limma_3.44.3.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 https://bioconductor.org/packages/limma/
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