/usr/lib/R/site-library/limma/help/AnIndex is in r-bioc-limma 3.34.0+dfsg-1.
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01.Introduction 01Introduction
02.Classes 02classes
03.ReadingData 03reading
04.Background 04Background
05.Normalization 05Normalization
06.LinearModels 06linearmodels
07.SingleChannel 07SingleChannel
08.Tests 08Tests
09.Diagnostics 09Diagnostics
10.GeneSetTests 10GeneSetTests
11.RNAseq 11RNAseq
alias2Symbol alias2Symbol
alias2SymbolTable alias2Symbol
alias2SymbolUsingNCBI alias2Symbol
anova.MAList anova-method
array2channel targetsA2C
arrayWeights arrayWeights
arrayWeightsQuick arrayWeightsQuick
arrayWeightsSimple arrayWeights
as.data.frame.EList asdataframe
as.data.frame.EListRaw asdataframe
as.data.frame.MAList asdataframe
as.data.frame.MArrayLM asdataframe
as.MAList asmalist
as.matrix.EList asmatrix
as.matrix.EListRaw asmatrix
as.matrix.ExpressionSet asmatrix
as.matrix.LumiBatch asmatrix
as.matrix.MAList asmatrix
as.matrix.MArrayLM asmatrix
as.matrix.marrayNorm asmatrix
as.matrix.PLMset asmatrix
as.matrix.RGList asmatrix
as.matrix.vsn asmatrix
asMatrixWeights asMatrixWeights
auROC auROC
avearrays avearrays
avearrays.default avearrays
avearrays.EList avearrays
avearrays.MAList avearrays
avedups avedups
avedups.default avedups
avedups.EList avedups
avedups.MAList avedups
avereps avereps
avereps.default avereps
avereps.EList avereps
avereps.EListRaw avereps
avereps.MAList avereps
avereps.RGList avereps
backgroundCorrect backgroundcorrect
backgroundCorrect.matrix backgroundcorrect
barcodeplot barcodeplot
beadCountWeights beadCountWeights
blockDiag blockDiag
bwss bwss
bwss.matrix bwss.matrix
camera camera
camera.default camera
cameraPR camera
cameraPR.default camera
cbind cbind
cbind.EList cbind
cbind.EListRaw cbind
cbind.MAList cbind
cbind.RGList cbind
changeLog changelog
classifyTestsF classifytests
classifyTestsP classifytests
classifyTestsT classifytests
coerce,RGList,exprSet2-method rglist
contrastAsCoef contrastAsCoef
contrasts.fit contrasts.fit
controlStatus controlStatus
convest propTrueNull
coolmap coolmap
cumOverlap cumOverlap
decideTests decideTests
decideTests.default decideTests
decideTests.MArrayLM decideTests
designI2A channel2M
designI2M channel2M
detectionPValues detectionPValue
detectionPValues.default detectionPValue
detectionPValues.EListRaw detectionPValue
diffSplice diffSplice
dim.EList dim
dim.EListRaw dim
dim.MAList dim
dim.MArrayLM dim
dim.RGList dim
dimnames.EList dimnames
dimnames.EListRaw dimnames
dimnames.MAList dimnames
dimnames.MArrayLM dimnames
dimnames.RGList dimnames
dimnames<-.EList dimnames
dimnames<-.EListRaw dimnames
dimnames<-.MAList dimnames
dimnames<-.RGList dimnames
duplicateCorrelation dupcor
eBayes ebayes
ebayes ebayes
EList-class EList
EListRaw-class EList
estimate.m0 propTrueNull
exprs.MA exprsMA
fitFDist fitfdist
fitFDistRobustly fitfdist
fitGammaIntercept fitGammaIntercept
fitmixture fitmixture
fitted.MArrayLM fitted.MArrayLM
fry roast
fry.default roast
FStat classifytests
genas genas
geneSetTest geneSetTest
getDupSpacing getlayout
getEAWP getEAWP
getGeneKEGGLinks goana
getKEGGPathwayNames goana
getLayout getlayout
getLayout2 getlayout
getSpacing getSpacing
gls.series gls.series
goana goana
goana.default goana
goana.MArrayLM goana
gridc gridspotrc
gridr gridspotrc
heatDiagram heatdiagram
heatdiagram heatdiagram
helpMethods helpMethods
ids2indices ids2indices
imageplot imageplot
imageplot3by2 imageplot3by2
interGeneCorrelation camera
intraspotCorrelation intraspotCorrelation
is.fullrank isfullrank
isNumeric isnumeric
kegga goana
kegga.default goana
kegga.MArrayLM goana
kooperberg kooperberg
LargeDataObject-class LargeDataObject
limma 01Introduction
limmaUsersGuide limmaUsersGuide
lm.series lm.series
lmFit lmFit
lmscFit lmscFit
loessFit loessfit
logcosh logcosh
MA.RG normalizeWithinArrays
ma3x3.matrix ma3x3
ma3x3.spottedarray ma3x3
makeContrasts makeContrasts
makeUnique makeunique
MAList-class malist
MArrayLM-class marraylm
mdplot mdplot
MDS-class plotMDS
merge.EList merge
merge.EListRaw merge
merge.MAList merge
merge.RGList merge
mergeScans mergeScansRG
mergeScansRG mergeScansRG
modelMatrix modelMatrix
modifyWeights modifyWeights
mrlm mrlm
mroast roast
mroast.default roast
nec nec
neqc nec
nonEstimable isfullrank
normalizeBetweenArrays normalizebetweenarrays
normalizeCyclicLoess normalizeCyclicLoess
normalizeForPrintorder normalizeprintorder
normalizeForPrintorder.rg normalizeprintorder
normalizeMedianAbsValues normalizeMedianAbsValues
normalizeMedianValues normalizeMedianAbsValues
normalizeQuantiles normalizequantiles
normalizeRobustSpline normalizeRobustSpline
normalizeVSN normalizeVSN
normalizeVSN.default normalizeVSN
normalizeVSN.EListRaw normalizeVSN
normalizeVSN.RGList normalizeVSN
normalizeWithinArrays normalizeWithinArrays
normexp.fit normexpfit
normexp.fit.control normexpfitcontrol
normexp.fit.detection.p normexpfitdetectionp
normexp.signal normexpsignal
plotDensities plotDensities
plotDensities.default plotDensities
plotDensities.EList plotDensities
plotDensities.EListRaw plotDensities
plotDensities.MAList plotDensities
plotDensities.RGList plotDensities
plotExons plotExons
plotFB plotFB
plotFB.default plotFB
plotFB.EListRaw plotFB
plotFB.RGList plotFB
plotlines plotlines
plotMA plotma
plotMA.default plotma
plotMA.EList plotma
plotMA.EListRaw plotma
plotMA.MAList plotma
plotMA.MArrayLM plotma
plotMA.RGList plotma
plotMA3by2 plotma3by2
plotMD plotMD
plotMD.default plotMD
plotMD.EList plotMD
plotMD.EListRaw plotMD
plotMD.MAList plotMD
plotMD.MArrayLM plotMD
plotMD.RGList plotMD
plotMDS plotMDS
plotMDS.default plotMDS
plotMDS.MDS plotMDS
plotPrintorder normalizeprintorder
plotPrintTipLoess plotprinttiploess
plotRLDF plotRLDF
plotSA plotSA
plotSplice plotSplice
plotWithHighlights plotWithHighlights
poolVar poolvar
predFCm predFCm
printHead printHead
PrintLayout-class PrintLayout
printorder printorder
printtipWeights printtipWeights
printtipWeightsSimple printtipWeights
propexpr propexpr
propTrueNull propTrueNull
protectMetachar protectMetachar
qqf qqt
qqt qqt
QualityWeights qualwt
rankSumTestWithCorrelation rankSumTestwithCorrelation
rbind.EList cbind
rbind.EListRaw cbind
rbind.MAList cbind
rbind.RGList cbind
read.columns read.columns
read.idat read.idat
read.ilmn read.ilmn
read.ilmn.targets read.ilmn.targets
read.imagene read.maimages
read.maimages read.maimages
readGAL readgal
readGenericHeader readGPRHeader
readGPRHeader readGPRHeader
readImaGeneHeader readImaGeneHeader
readSMDHeader readGPRHeader
readSpotTypes readSpotTypes
readTargets readTargets
removeBatchEffect removeBatchEffect
removeExt removeext
residuals.MArrayLM residuals.MArrayLM
RG.MA normalizeWithinArrays
RGList-class rglist
roast roast
Roast-class roast
roast.default roast
romer romer
romer.default romer
selectModel selectmodel
show,LargeDataObject-method LargeDataObject
show,MDS-method plotMDS
show,Roast-method roast
show,TestResults-method TestResults
spotc gridspotrc
spotr gridspotrc
squeezeVar squeezeVar
strsplit2 strsplit2
subsetListOfArrays subsetting
subsetting subsetting
summary.EList summary
summary.EListRaw summary
summary.MAList summary
summary.MArrayLM summary
summary.RGList summary
summary.TestResults TestResults
targetsA2C targetsA2C
TestResults-class TestResults
tmixture.matrix tmixture
tmixture.vector tmixture
topGO topGO
topKEGG topGO
topRomer topRomer
topSplice topSplice
topTable toptable
toptable toptable
topTableF toptable
topTreat toptable
treat ebayes
tricubeMovingAverage tricubeMovingAverage
trigammaInverse trigammainverse
trimWhiteSpace trimWhiteSpace
tZscore zscore
uniquegenelist uniquegenelist
uniqueTargets modelMatrix
unwrapdups unwrapdups
vennCounts venn
vennDiagram venn
volcanoplot volcanoplot
voom voom
vooma vooma
voomaByGroup vooma
voomWithQualityWeights voomWithQualityWeights
weighted.median weightedmedian
weightedLowess weightedLowess
wilcoxGST geneSetTest
write.fit writefit
wsva wsva
wtarea qualwt
wtflags qualwt
wtIgnore.Filter qualwt
zscore zscore
zscoreGamma zscore
zscoreHyper zscore
zscoreT zscore
[.EList subsetting
[.EListRaw subsetting
[.MAList subsetting
[.MArrayLM subsetting
[.RGList subsetting
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