addIdQvalues	addIdQvalues
addScaffoldPTMFAnnotations	addScaffoldPTMFAnnotations
barplotMSSignal	barplotMSSignal
COLORS	COLORS
createExpDesign	createExpDesign
createExpressionDataset	createExpressionDataset
createPairedExpDesign	createPairedExpDesign
cvBoxplot	cvBoxplot
expDesignTagToExpDesign	expDesignTagToExpDesign
export	export
getAAProteinCoordinates	getAAProteinCoordinates
getAllCV	getAllCV
getAllEBayes	getAllEBayes
getBaselineIntensity	getBaselineIntensity
getCV	getCV
getExpDesignProgenesisCsv	getExpDesignProgenesisCsv
getGlobalNormFactors	getGlobalNormFactors
getIBAQEset	getIBAQEset
getIdLevelQvals	getIdLevelQvals
getImpuritiesMatrix	getImpuritiesMatrix
getIntSumPerProtein	getIntSumPerProtein
getLoocvFoldError	getLoocvFoldError
getMaxIndex	getMaxIndex
getMeanCenteredRange	getMeanCenteredRange
getModifProteinCoordinates	getModifProteinCoordinates
getMotifX	getMotifX
getNbDetectablePeptides	getNbDetectablePeptides
getNbMisCleavages	getNbMisCleavages
getNbPeptidesPerProtein	getNbPeptidesPerProtein
getNbSpectraPerProtein	getNbSpectraPerProtein
getPeptides	getPeptides
getRatios	getRatios
getRTNormFactors	getRTNormFactors
getScoreCutOff	getScoreCutOff
getSignalPerCondition	getSignalPerCondition
getTopX	getTopX
getUserOptions	getUserOptions
globalNormalize	globalNormalize
hClustHeatMap	hClustHeatMap
isCon	isCon
isDecoy	isDecoy
isStrippedACs	isStrippedACs
maPlotSQ	maPlotSQ
missinValueBarplot	missinValueBarplot
option_list	option_list
pairsAnnot	pairsAnnot
parseMaxQuantProteinGroupTxt	parseMaxQuantProteinGroupTxt
parseProgenesisFeatureCsv	parseProgenesisFeatureCsv
parseProgenesisPeptideMeasurementCsv	parseProgenesisPeptideMeasurementCsv
parseProgenesisProteinCsv	parseProgenesisProteinCsv
parseScaffoldPTMReport	parseScaffoldPTMReport
parseScaffoldRawFile	parseScaffoldRawFile
perFeatureNormalization	perFeatureNormalization
plotAbsEstCalibrationCurve	plotAbsEstCalibrationCurve
plotAdjustedVsNonAdjustedRatio	plotAdjustedVsNonAdjustedRatio
plotExpDesign	plotExpDesign
plotIdScoreVsFDR	plotIdScoreVsFDR
plotMSSignalDistributions	plotMSSignalDistributions
plotNbIdentificationsVsRT	plotNbIdentificationsVsRT
plotNbValidDeFeaturesPerFDR	plotNbValidDeFeaturesPerFDR
plotPrecMassErrorDistrib	plotPrecMassErrorDistrib
plotPrecMassErrorVsScore	plotPrecMassErrorVsScore
plotQValueVsPValue	plotQValueVsPValue
plotROC	plotROC
plotRTNorm	plotRTNorm
plotRTNormSummary	plotRTNormSummary
plotScoreDistrib	plotScoreDistrib
plotVolcano	plotVolcano
plotXYDensity	plotXYDensity
purityCorrectTMT	purityCorrectTMT
removeOutliers	removeOutliers
rollUp	rollUp
rtNormalize	rtNormalize
safeQuantAnalysis	safeQuantAnalysis
setNbPeptidesPerProtein	setNbPeptidesPerProtein
setNbSpectraPerProtein	setNbSpectraPerProtein
sqNormalize	sqNormalize
standardise	standardise
stripACs	stripACs
