DESeq2
Differential gene expression analysis based on the negative binomial distribution

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Functions
202
Source code
48
Man pages
41
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DESeq2: Differential gene expression analysis based on the negative binomial distribution
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API

API for DESeq2
Differential gene expression analysis based on the negative binomial distribution

Global functions
DESeq Man page Source code
DESeq2-package Man page
DESeqDataSet Man page Source code
DESeqDataSet-class Man page
DESeqDataSetFromHTSeqCount Man page Source code
DESeqDataSetFromMatrix Man page Source code
DESeqDataSetFromTximport Man page Source code
DESeqParallel Source code
DESeqResults Man page Source code
DESeqResults-class Man page
DESeqTransform Man page Source code
DESeqTransform-class Man page
Hmisc.wtd.Ecdf Source code
Hmisc.wtd.quantile Source code
Hmisc.wtd.table Source code
addAllContrasts Source code
averagePriorsOverLevels Source code
buildDataFrameWithNARows Source code
buildMatrixWithNARows Source code
buildMatrixWithZeroRows Source code
calculateCooksDistance Source code
checkContrast Source code
checkForExperimentalReplicates Source code
checkFullRank Source code
checkLRT Source code
cleanContrast Source code
coef Man page
coef.DESeqDataSet Man page Source code
collapseReplicates Man page Source code
contrastAllZeroCharacter Source code
contrastAllZeroNumeric Source code
counts Man page
counts,DESeqDataSet-method Man page
counts.DESeqDataSet Source code
counts<-,DESeqDataSet,matrix-method Man page
covarianceMatrix Source code
design Man page
design,DESeqDataSet-method Man page
design.DESeqDataSet Source code
design.replace Source code
design<-,DESeqDataSet,formula-method Man page
design<-,DESeqDataSet,matrix-method Man page
designAndArgChecker Source code
dispFun.replace Source code
dispersionFunction Man page
dispersionFunction,DESeqDataSet-method Man page
dispersionFunction.DESeqDataSet Source code
dispersionFunction<- Man page
dispersionFunction<-,DESeqDataSet,function-method Man page
dispersions Man page
dispersions,DESeqDataSet-method Man page
dispersions.DESeqDataSet Source code
dispersions<- Man page
dispersions<-,DESeqDataSet,numeric-method Man page
estimateBetaPriorVar Man page Source code
estimateDispersions Man page
estimateDispersions,DESeqDataSet-method Man page
estimateDispersions.DESeqDataSet Source code
estimateDispersionsFit Man page Source code
estimateDispersionsGeneEst Man page Source code
estimateDispersionsMAP Man page Source code
estimateDispersionsPriorVar Man page Source code
estimateMLEForBetaPriorVar Man page Source code
estimateNormFactors Source code
estimateSizeFactors Man page
estimateSizeFactors,DESeqDataSet-method Man page
estimateSizeFactors.DESeqDataSet Source code
estimateSizeFactorsForMatrix Man page Source code
estimateSizeFactorsIterate Source code
fitBeta Source code
fitDisp Source code
fitDispGrid Source code
fitDispGridWrapper Source code
fitGLMsWithPrior Source code
fitNbinomGLMs Source code
fitNbinomGLMsOptim Source code
fpkm Man page Source code
fpm Man page Source code
getAndCheckWeights Source code
getBaseMeansAndVariances Source code
getCoef Source code
getCoefSE Source code
getContrast Source code
getDesignFactors Source code
getModelMatrix Source code
getNworkers Source code
getPvalue Source code
getSizeOrNormFactors Source code
getStat Source code
getVarianceStabilizedData Man page Source code
integrateWithSingleCell Man page Source code
lastCoefName Source code
lfcShrink Man page Source code
linearModelMu Source code
linearModelMuNormalized Source code
localDispersionFit Source code
makeExampleDESeqDataSet Man page Source code
makeExpandedModelMatrix Source code
makeWaldTest Source code
matchUpperQuantileForVariance Source code
matchWeightedUpperQuantileForVariance Source code
matrixToList Source code
mleContrast Source code
modelMatrixGroups Source code
momentsDispEstimate Source code
nOrMoreInCell Source code
nbinomLRT Man page Source code
nbinomLogLike Source code
nbinomWaldTest Man page Source code
normTransform Man page Source code
normalizationFactors Man page
normalizationFactors,DESeqDataSet-method Man page
normalizationFactors.DESeqDataSet Source code
normalizationFactors<- Man page
normalizationFactors<-,DESeqDataSet,matrix-method Man page
normalizeGeneLength Man page Source code
parametricDispersionFit Source code
plotCounts Man page Source code
plotDispEsts Man page
plotDispEsts,DESeqDataSet-method Man page
plotDispEsts.DESeqDataSet Source code
plotMA Man page
plotMA,DESeqDataSet-method Man page
plotMA,DESeqResults-method Man page
plotMA.DESeqDataSet Source code
plotMA.DESeqResults Source code
plotPCA Man page
plotPCA,DESeqTransform-method Man page
plotPCA.DESeqTransform Source code
plotSparsity Man page Source code
priorInfo Man page
priorInfo,DESeqResults-method Man page
priorInfo<- Man page
priorInfo<-,DESeqResults,list-method Man page
processTximeta Source code
pvalueAdjustment Source code
recordMaxCooks Source code
refitWithoutOutliers Source code
removeResults Man page Source code
renameModelMatrixColumns Source code
replaceOutliers Man page Source code
replaceOutliersWithTrimmedMean Man page
results Man page Source code
resultsFormatSwitch Source code
resultsNames Man page Source code
rlog Man page Source code
rlogData Source code
rlogTransformation Man page
robustMethodOfMomentsDisp Source code
roughDispEstimate Source code
sanitizeColData Source code
sanitizeRowRanges Source code
show Man page
show,DESeqResults-method Man page
sizeFactors Man page
sizeFactors,DESeqDataSet-method Man page
sizeFactors.DESeqDataSet Source code
sizeFactors<-,DESeqDataSet,numeric-method Man page
sparseTest Source code
summary Man page
summary,DESeqResults-method Man page
summary.DESeqResults Source code
trimmedCellVariance Source code
trimmedVariance Source code
unmix Man page Source code
varianceStabilizingTransformation Man page
vst Man page Source code
DESeq2 documentation built on Feb. 22, 2021, 10 a.m.

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