API for aghozlane/DESeq2shaman
Differential gene expression analysis based on the negative binomial distribution

Global functions
DESeq Man page Source code
DESeqDataSet Man page Source code
DESeqDataSet-class Man page
DESeqDataSetFromHTSeqCount Man page Source code
DESeqDataSetFromMatrix Man page Source code
DESeqParallel Source code
DESeqResults Man page Source code
DESeqResults-class Man page
addAllContrasts Source code
allFactors Source code
averagePriorsOverLevels Source code
buildDataFrameWithNARows Source code
buildMatrixWithNARows Source code
buildMatrixWithZeroRows Source code
buildNumericWithNARows Source code
buildNumericWithZeroRows Source code
calculateCooksDistance Source code
checkLRT Source code
cleanContrast Source code
coef Man page
coef.DESeqDataSet Man page Source code
col2useful Source code
collapseReplicates Man page Source code
counts Man page
counts,DESeqDataSet-method Man page
counts.DESeqDataSet Man page Source code
counts<-,DESeqDataSet,matrix-method Man page
covarianceMatrix Source code
design Man page
design,DESeqDataSet-method Man page
design.DESeqDataSet Man page Source code
design<-,DESeqDataSet,formula-method Man page
dispersionFunction Man page
dispersionFunction,DESeqDataSet-method Man page
dispersionFunction.DESeqDataSet Man page Source code
dispersionFunction<- Man page
dispersionFunction<-,DESeqDataSet,function-method Man page
dispersions Man page
dispersions,DESeqDataSet-method Man page
dispersions.DESeqDataSet Man page 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 Man page 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 Man page Source code
estimateSizeFactorsForMatrix Man page Source code
factorPresentThreeOrMoreLevels Source code
fitBeta Source code
fitDisp Source code
fitDispGrid Source code
fitDispGridWrapper Source code
fitDispInR Source code
fitGLMsWithPrior Source code
fitNbinomGLMs Source code
fitNbinomGLMsOptim Source code
fpkm Man page Source code
fpm Man page Source code
getBaseMeansAndVariances Source code
getCoef Source code
getCoefSE Source code
getContrast Source code
getDesignFactors Source code
getNonInteractionColumnIndices Source code
getPvalue Source code
getStat Source code
getVarianceStabilizedData Man page Source code
lastCoefName Source code
leaveOneOutFullRank Source code
linearModelMu 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
medianCellVariance Source code
mleContrast Source code
momentsDispEstimate Source code
nOrMoreInCell Source code
nbinomLRT Man page Source code
nbinomLogLike Source code
nbinomWaldTest Man page Source code
normalizationFactors Man page
normalizationFactors,DESeqDataSet-method Man page
normalizationFactors.DESeqDataSet Man page Source code
normalizationFactors<- Man page
normalizationFactors<-,DESeqDataSet,matrix-method Man page
pAdjustWithIndependentFiltering Source code
parametricDispersionFit Source code
plotCounts Man page Source code
plotDispEsts Man page
plotDispEsts,DESeqDataSet-method Man page
plotDispEsts.DESeqDataSet Man page Source code
plotMA Man page
plotMA,DESeqDataSet-method Man page
plotMA,DESeqResults-method Man page
plotMA.DESeqDataSet Man page Source code
plotMA.DESeqResults Source code
plotPCA Man page Source code
propMaxOfTotal 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
resultsNames Man page Source code
rlog Man page Source code
rlogData Source code
rlogDataFast Source code
rlogGrid Source code
rlogTransformation Man page
robustMethodOfMomentsDisp Source code
roughDispEstimate Source code
sanitizeColData Source code
sanitizeRowData Source code
show Man page
show,DESeqResults-method Man page
sizeFactors Man page
sizeFactors,DESeqDataSet-method Man page
sizeFactors.DESeqDataSet Man page Source code
sizeFactors<-,DESeqDataSet,numeric-method Man page
summary Man page
summary.DESeqResults Man page Source code
trimmedCellVariance Source code
trimmedVariance Source code
varianceStabilizingTransformation Man page
aghozlane/DESeq2shaman documentation built on Nov. 1, 2019, 9:01 p.m.