limma (original) (raw)

This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, seelimma.

Linear Models for Microarray Data

Bioconductor version: 2.12

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

Author: Gordon Smyth with contributions from Matthew Ritchie, Jeremy Silver, James Wettenhall, Natalie Thorne, Mette Langaas, Egil Ferkingstad, Marcus Davy, Francois Pepin, Dongseok Choi, Davis McCarthy, Di Wu, Alicia Oshlack, Carolyn de Graaf, Yifang Hu, Wei Shi and Belinda Phipson.

Maintainer: Gordon Smyth

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

Installation

To install this package, start R and enter:

try http:// if https:// URLs are not supported

source("https://bioconductor.org/biocLite.R") biocLite("limma")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("limma")

PDF R Script Limma Vignette
PDF usersguide.pdf
PDF Reference Manual
Text NEWS

Details

biocViews Bioinformatics, DataImport, DifferentialExpression, Microarray, MultipleComparisons, OneChannel, Preprocessing, QualityControl, Software, TimeCourse, TwoChannel
Version 3.16.8
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 11 years)
License GPL (>=2)
Depends R (>= 2.3.0), methods
Imports
LinkingTo
Suggests affy, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn, ellipse
SystemRequirements
Enhances
URL http://bioinf.wehi.edu.au/limma
Depends On Me a4Base, AffyExpress, affylmGUI, Agi4x44PreProcess, AgiMicroRna, attract, birta, CALIB, CCl4, cghMCR, ChIPpeakAnno, clippda, codelink, convert, Cormotif, coRNAi, DrugVsDisease, edgeR, ExiMiR, gCMAP, HD2013SGI, HTqPCR, limmaGUI, lmdme, LVSmiRNA, maDB, maigesPack, marray, metagenomeSeq, MmPalateMiRNA, nem, PADOG, qpcrNorm, Ringo, snapCGH, SSPA, TurboNorm, wateRmelon
Imports Me affycoretools, ArrayExpress, arrayQuality, arrayQualityMetrics, ArrayTools, attract, beadarray, BeadArrayUseCases, betr, bumphunter, CALIB, CancerMutationAnalysis, charm, ChIPpeakAnno, explorase, GeneSelectMMD, GeneSelector, GGBase, HTqPCR, iChip, maSigPro, minfi, MmPalateMiRNA, OLIN, PADOG, phenoTest, ReportingTools, Ringo, RNAinteract, RNAither, RTopper, snapCGH, timecourse, tweeDEseq, vsn
Suggests Me ABarray, beadarraySNP, BiocCaseStudies, BioNet, bumphunter, Category, categoryCompare, CMA, coGPS, dyebias, GeneSelector, GEOquery, GSRI, GSVA, Heatplus, inSilicoDb, isobar, les, lumi, methylumi, MLP, oligo, oneChannelGUI, PGSEA, piano, plw, PREDA, puma, Rcade, RTopper, rtracklayer, sva, virtualArray
Build Report

Package Archives

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

Package Source limma_3.16.8.tar.gz
Windows Binary limma_3.16.8.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) limma_3.16.8.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/limma/tree/release-2.12
Package Short Url http://bioconductor.org/packages/limma/
Package Downloads Report Download Stats