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Bioconductor - limma (development version)

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 (3.22)

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")

# The following initializes usage of Bioc devel
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")

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 3.65.1 In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 20 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/ See More 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, GEOexplorer, 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, arrayQualityMetrics, artMS, ATACseqQC, ATACseqTFEA, attract, autonomics, AWFisher, ballgown, barbieQ, BatchQC, beadarray, BERT, biotmle, BloodGen3Module, bnem, bsseq, BubbleTree, bumphunter, casper, ChAMP, CleanUpRNAseq, clusterExperiment, CNVRanger, combi, compcodeR, consensusDE, consensusOV, crlmm, csaw, cTRAP, ctsGE, DAMEfinder, DaMiRseq, debrowser, DELocal, DEP, derfinderPlot, DESpace, DEsubs, DExMA, DiffBind, diffcyt, diffHic, diffUTR, distinct, DMRcate, Doscheda, dreamlet, DRIMSeq, 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, 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, NADfinder, NanoMethViz, nethet, nondetects, NormalyzerDE, OLIN, omicRexposome, OVESEG, PAA, PADOG, pairedGSEA, PanomiR, PathoStat, pcaExplorer, PECA, PepSetTest, pepStat, phantasus, phenomis, phenoTest, PhosR, PolySTest, POMA, projectR, PRONE, psichomics, qmtools, qPLEXanalyzer, qsea, RegEnrich, regsplice, RFLOMICS, RNAseqCovarImpute, roastgsa, ROSeq, RTN, RTopper, saseR, satuRn, scClassify, scone, scQTLtools, scran, ScreenR, scviR, seqsetvis, shinyDSP, shinyepico, SingleCellSignalR, 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, CIDER, cinaR, DiPALM, dsb, eLNNpairedCov, Grouphmap, GSEMA, GWASbyCluster, inDAGO, 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 Suggests Me ABarray, ADaCGH2, Biobase, biobroom, BiocSet, BioNet, BioQC, broadSeq, Category, categoryCompare, 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, lute, methylumi, MLP, npGSEA, oligo, oppar, piano, PREDA, proDA, puma, QFeatures, qsvaR, raer, randRotation, recountmethylation, ribosomeProfilingQC, rtracklayer, Rvisdiff, signifinder, spatialHeatmap, SpliceWiz, stageR, subSeq, systemPipeR, tadar, TCGAbiolinks, 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, 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

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