addZeroTime	addZeroTime
calcKinaseScore	calcKinaseScore
checkRatioMat	checkRatioMat
clusterEnrich	clusterEnrich
clusterTS	clusterTS
dda_example	dda_example
dia_example	dia_example
enrichDifferential	enrichDifferential
generateInputTable	generateInputTable
generateInputTable_DIA	generateInputTable_DIA
getDecouplerNetwork	getDecouplerNetwork
getOneSymbol	getOneSymbol
getRatioMatrix	getRatioMatrix
Homo_sapien_kinase_substrate_network	Homo_sapien_kinase_substrate_network
intensityBoxPlot	intensityBoxPlot
makeSmartPhosDirectory	makeSmartPhosDirectory
medianNorm	medianNorm
mscale	mscale
Mus_musculus_kinase_substrate_network	Mus_musculus_kinase_substrate_network
normByFullProteome	normByFullProteome
performCombinedNormalization	performCombinedNormalization
performDifferentialExp	performDifferentialExp
plotAdjustmentResults	plotAdjustmentResults
plotHeatmap	plotHeatmap
plotIntensity	plotIntensity
plotKinaseDE	plotKinaseDE
plotKinaseTimeSeries	plotKinaseTimeSeries
plotLogRatio	plotLogRatio
plotMissing	plotMissing
plotPCA	plotPCA
plotTimeSeries	plotTimeSeries
plotVolcano	plotVolcano
preprocessPhos	preprocessPhos
preprocessProteome	preprocessProteome
readExperiment	readExperiment
readExperimentDIA	readExperimentDIA
readOnePhos	readOnePhos
readOnePhosDIA	readOnePhosDIA
readOneProteom	readOneProteom
readOneProteomDIA	readOneProteomDIA
readPhosphoExperiment	readPhosphoExperiment
readPhosphoExperimentDIA	readPhosphoExperimentDIA
readProteomeExperiment	readProteomeExperiment
readProteomeExperimentDIA	readProteomeExperimentDIA
runFisher	runFisher
runGSEAforPhospho	runGSEAforPhospho
runPhosphoAdjustment	runPhosphoAdjustment
runSmartPhos	runSmartPhos
splineFilter	splineFilter
swissProt	swissProt
