limma

Linear Models for Microarray and Omics Data

Bioconductor version: 3.23 · Package version: 3.68.4

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

Installation

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

BiocManager::install("limma")

Details

Maintainer	Gordon Smyth <smyth@wehi.edu.au>
Author	Gordon Smyth [cre, aut] (ORCID: <https://orcid.org/0000-0001-9221-2892>), 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] (ORCID: <https://orcid.org/0000-0002-8326-6781>)
License	GPL (>=2)
URL	https://bioinf.wehi.edu.au/limma/
Downloads rank	41961
Source branch	RELEASE_3_23
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

Documentation

Download

Source package

Dependencies

Depends: R (>= 3.6.0)

Imports: grDevices, graphics, stats, utils, methods, statmod

Suggests: BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines, affy, AnnotationDbi, Biobase, BiocStyle, GO.db, illuminaio, org.Hs.eg.db, vsn

Reverse dependencies

Depends On Me (55): AgiMicroRna, ASpli, BALLI, BioInsight, BLMA, CCl4, CEDA, cghMCR, ChimpHumanBrainData, clippda, codelink, convert, Cormotif, cp4p, DAAGbio, DEqMS, DRomics, DrugVsDisease, edgeR, EGSEA123, ExiMiR, ExpressionAtlas, Fletcher2013a, fmt, GEOexplorer, HD2013SGI, HTqPCR, IsoformSwitchAnalyzeR, limpa, maPredictDSC, marray, metagenomeSeq, metaseqR2, methylationArrayAnalysis, mpra, NanoTube, octad, PerfMeas, protGear, qpcrNorm, qusage, RBM, ReactomeGSA.data, RNAseq123, RnBeads, Rnits, splineTimeR, TMSig, TOAST, tRanslatome, ttScreening, TurboNorm, variancePartition, wateRmelon, zenith

Imports Me (264): a4Base, ABSSeq, affycoretools, affylmGUI, AMARETTO, animalcules, anota2seq, ArrayExpress, arrayQuality, arrayQualityMetrics, artMS, ATACseqQC, ATACseqTFEA, attract, autonomics, AWFisher, ballgown, barbieQ, BatChef, BatchQC, batchtma, beadarray, BeadArrayUseCases, benchdamic, BERT, biotmle, BioUtils, BloodGen3Module, bnem, BPM, bsseq, BubbleTree, bumphunter, Cascade, casper, ChAMP, ChIPComp, cinaR, CleanUpRNAseq, clusterExperiment, CNVRanger, combi, compcodeR, CONFESS, consensusOV, crlmm, csaw, cTRAP, ctsGE, DAMEfinder, damidBind, DaMiRseq, debrowser, DeeDeeExperiment, DELocal, derfinderPlot, DESpace, DEsubs, DExMA, DiffBind, diffcyt, diffHic, diffUTR, DiPALM, distinct, DMRcate, Doscheda, dreamlet, DRIMSeq, dsb, DspikeIn, EGAD, EGSEA, eisaR, eLNNpairedCov, EnrichmentBrowser, epigraHMM, EpiMix, erccdashboard, EventPointer, EWCE, ExpHunterSuite, ExploreModelMatrix, ExpressionNormalizationWorkflow, flowBin, gCrisprTools, GDCRNATools, genefu, GeneSelectMMD, GEOquery, gg4way, gINTomics, Glimma, GRaNIE, 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, 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, moanin, monocle, MoonlightR, MSclassifR, msImpute, mspms, msqrob2, MSstats, MSstatsTMT, MultiDataSet, 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, psichomics, qmtools, qPLEXanalyzer, qsea, RANKS, rCGH, RCPA, recountWorkflow, RegEnrich, regsplice, ReportingTools, RFGeneRank, RFLOMICS, RNAseqCovarImpute, roastgsa, robusttseq, ROSeq, RPPanalyzer, RTN, RTopper, saseR, satuRn, scBio, scClassify, scGOclust, scone, scQTLtools, scran, ScreenR, scROSHI, scviR, seqsetvis, shinyDSP, shinyepico, signatureSearchData, singleCellTK, SmartPhos, sparrow, spatialLIBD, speckle, SpNeigh, SPsimSeq, ssizeRNA, standR, STATegRa, Statial, structToolbox, sva, tidyexposomics, timecourse, tinyarray, TOP, ToxicoGx, TPP, TPP2D, transcriptogramer, TransProR, treediff, TVTB, tweeDEseq, unifiedWMWqPCR, VISTA, vsclust, vsn, weitrix, Wrench, wrProteo, XAItest, XYomics, yamss, yarn

Suggests Me (118): ABarray, ADaCGH2, AnnoProbe, aroma.affymetrix, arrays, Biobase, biobroom, BiocSet, BioNet, BioQC, blase, BloodCancerMultiOmics2017, broadSeq, bugphyzz, CAGEWorkflow, canvasXpress, Category, categoryCompare, celaref, CellBench, CellMixS, ChIPpeakAnno, ClassifyR, CMA, coGPS, CONSTANd, corncob, cydar, Damsel, DAPAR, dar, 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, limorhyde, lionessR, lumi, maGUI, mammaPrintData, MAST, methylumi, MLP, MosaiClusteR, msigdb, NACHO, 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