analyzeNormalizations	analyzeNormalizations
calculateANOVAPValues	calculateANOVAPValues
calculateAvgMadMem	calculateAvgMadMem
calculateAvgReplicateVariation	calculateAvgReplicateVariation
calculateContrasts	calculateContrasts
calculateContrasts,NormalyzerStatistics-method	calculateContrasts
calculateCorrSum	calculateCorrSum
calculateFeatureCV	calculateFeatureCV
calculatePercentageAvgDiffInMat	calculatePercentageAvgDiffInMat
calculateReplicateCV	calculateReplicateCV
calculateSummarizedCorrelationVector	calculateSummarizedCorrelationVector
createDirectory	createDirectory
detectSingleReplicate	detectSingleReplicate
detectSingleReplicate,NormalyzerDataset-method	detectSingleReplicate
detectSingletonSample	detectSingletonSample
detectSingletonSample,NormalyzerDataset-method	detectSingletonSample
elapsedSecondsBetweenSystimes	elapsedSecondsBetweenSystimes
example_data	example_data
example_data_only_values	example_data_only_values
example_design	example_design
example_stat_data	example_stat_data
example_stat_summarized_experiment	example_stat_summarized_experiment
example_summarized_experiment	example_summarized_experiment
example_wide_data	example_wide_data
example_wide_design	example_wide_design
filterLowRep	filterLowRep
findLowlyVariableFeaturesCVs	findLowlyVariableFeaturesCVs
generateAnnotatedMatrix	generateAnnotatedMatrix
generatePlots	generatePlots
generateStatsReport	generateStatsReport
getCombinedMatrix	getCombinedMatrix
getIndexList	getIndexList
getLowCountSampleFiltered	getLowCountSampleFiltered
getReplicateSortedData	getReplicateSortedData
getRowNAFilterContrast	getRowNAFilterContrast
getRTNormalizedMatrix	getRTNormalizedMatrix
getSmoothedRTNormalizedMatrix	getSmoothedRTNormalizedMatrix
getVerifiedNormalyzerObject	getVerifiedNormalyzerObject
getWidenedRTRange	getWidenedRTRange
globalIntensityNormalization	globalIntensityNormalization
loadData	loadData
loadDesign	loadDesign
loadRawDataFromFile	loadRawDataFromFile
meanNormalization	meanNormalization
medianNormalization	medianNormalization
normalyzer	normalyzer
NormalyzerDataset	NormalyzerDataset
normalyzerDE	normalyzerDE
NormalyzerEvaluationResults	NormalyzerEvaluationResults
NormalyzerResults	NormalyzerResults
NormalyzerStatistics	NormalyzerStatistics
normMethods	normMethods
performCyclicLoessNormalization	performCyclicLoessNormalization
performGlobalRLRNormalization	performGlobalRLRNormalization
performNoNormalization	performNoNormalization
performNormalizations	performNormalizations
performNormalizations,NormalyzerResults-method	performNormalizations
performQuantileNormalization	performQuantileNormalization
performSMADNormalization	performSMADNormalization
performVSNNormalization	performVSNNormalization
plotBoxPlot	plotBoxPlot
plotComparisonVenns	plotComparisonVenns
plotContrastPCA	plotContrastPCA
plotContrastPHists	plotContrastPHists
plotCorrelation	plotCorrelation
plotCVvsIntensity	plotCVvsIntensity
plotDendrograms	plotDendrograms
plotDensity	plotDensity
plotFrontPage	plotFrontPage
plotMA	plotMA
plotMDS	plotMDS
plotMeanSD	plotMeanSD
plotPHist	plotPHist
plotQQ	plotQQ
plotReplicateVarAndStableVariables	plotReplicateVarAndStableVariables
plotReplicateVariance	plotReplicateVariance
plotRLE	plotRLE
plotSampleMappingPage	plotSampleMappingPage
plotSampleOutlierSummary	plotSampleOutlierSummary
plotScatter	plotScatter
plotSigScatter	plotSigScatter
preprocessData	preprocessData
printMeta	printMeta
printPlots	printPlots
reduceTechnicalReplicates	reduceTechnicalReplicates
setupJobDir	setupJobDir
setupPlotting	setupPlotting
setupRawContrastObject	setupRawContrastObject
setupRawDataObject	setupRawDataObject
setupTestData	setupTestData
validateSampleReplication	validateSampleReplication
verifyContrasts	verifyContrasts
verifyDesignMatrix	verifyDesignMatrix
verifyMultipleSamplesPresent	verifyMultipleSamplesPresent
verifySummarizedExperiment	verifySummarizedExperiment
verifyValidNumbers	verifyValidNumbers
writeNormalizedDatasets	writeNormalizedDatasets
