This package is for version 3.4 of Bioconductor;
for the stable, up-to-date release version, see
limma.
Linear Models for Microarray Data
Bioconductor version: 3.4
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 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
Limma One Page Introduction
Details
biocViews
AlternativeSplicing,
BatchEffect,
Bayesian,
Clustering,
DataImport,
DifferentialExpression,
DifferentialSplicing,
ExonArray,
GeneExpression,
GeneSetEnrichment,
Genetics,
Microarray,
MultipleComparison,
Normalization,
OneChannel,
Preprocessing,
ProprietaryPlatforms,
QualityControl,
RNASeq,
Regression,
Software,
TimeCourse,
Transcription,
TwoChannel,
mRNAMicroarray,
microRNAArray
Version
3.30.13
In Bioconductor since
BioC 1.6 (R-2.1) or earlier (> 12 years)
License
GPL (>=2)
Depends
R (>= 2.3.0)
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
Depends On Me
a4Base,
AffyExpress,
AgiMicroRna,
birta,
bsseq,
CALIB,
CCl4,
cghMCR,
ChimpHumanBrainData,
clippda,
codelink,
convert,
Cormotif,
coRNAi,
DrugVsDisease,
edgeR,
ExiMiR,
ExpressionAtlas,
FEM,
Fletcher2013a,
gCMAP,
genefu,
HD2013SGI,
HTqPCR,
maigesPack,
maPredictDSC,
marray,
metagenomeSeq,
metaseqR,
MLSeq,
MmPalateMiRNA,
PGPC,
prot2D,
qpcrNorm,
qusage,
RBM,
Ringo,
RnBeads,
Rnits,
snapCGH,
splineTimeR,
SRGnet,
SSPA,
tRanslatome,
TurboNorm,
wateRmelon
Imports Me
ABSSeq,
affycoretools,
affylmGUI,
anamiR,
ArrayExpress,
arrayQuality,
arrayQualityMetrics,
ArrayTools,
attract,
ballgown,
BatchQC,
beadarray,
BeadArrayUseCases,
betr,
birte,
BubbleTree,
bumphunter,
CALIB,
CancerMutationAnalysis,
CancerSubtypes,
casper,
ChAMP,
charm,
ChIPComp,
ChIPpeakAnno,
clusterExperiment,
compcodeR,
CONFESS,
CountClust,
crlmm,
crossmeta,
csaw,
ctsGE,
DAPAR,
debrowser,
derfinderPlot,
DEsubs,
DiffBind,
diffHic,
diffloop,
DmelSGI,
DMRcate,
EBSEA,
eegc,
EGAD,
EGSEA,
EnrichmentBrowser,
erccdashboard,
explorase,
flowBin,
gCrisprTools,
GeneSelectMMD,
GeneSelector,
GGBase,
GOsummaries,
gQTLstats,
GUIDEseq,
HTqPCR,
iCheck,
iChip,
iCOBRA,
InPAS,
limmaGUI,
Linnorm,
lmdme,
LVSmiRNA,
mAPKL,
MEAL,
methylKit,
MethylMix,
minfi,
miRLAB,
missMethyl,
MmPalateMiRNA,
monocle,
MoonlightR,
MSstats,
nem,
nethet,
nondetects,
OGSA,
OLIN,
PAA,
PADOG,
PathoStat,
pbcmc,
pcaExplorer,
PECA,
pepStat,
phenoTest,
polyester,
qsea,
rCGH,
regsplice,
ReportingTools,
Ringo,
RNAinteract,
RNAither,
RTCGAToolbox,
RTN,
RTopper,
scater,
sigaR,
SimBindProfiles,
snapCGH,
STATegRa,
SVAPLSseq,
systemPipeR,
TCGAbiolinks,
timecourse,
ToPASeq,
TPP,
tweeDEseq,
variancePartition,
vsn,
yamss,
yarn
Suggests Me
ABarray,
ADaCGH2,
beadarraySNP,
biobroom,
BiocCaseStudies,
BioNet,
Category,
categoryCompare,
ClassifyR,
CMA,
coGPS,
derfinder,
dyebias,
ELBOW,
gage,
GeneSelector,
GEOquery,
GeuvadisTranscriptExpr,
Glimma,
GSRI,
GSVA,
Harman,
Heatplus,
isobar,
les,
lumi,
mammaPrintData,
MAST,
mdgsa,
methylumi,
MLP,
npGSEA,
oligo,
oneChannelGUI,
oppar,
paxtoolsr,
PGSEA,
piano,
plw,
PREDA,
puma,
Rcade,
RTopper,
rtracklayer,
scran,
seventyGeneData,
subSeq,
sva,
tximport
Package Archives
Follow
Installation instructions to use this
package in your R session.