cbind	PhosphoExperiment-operate
cbind,PhosphoExperiment-method	PhosphoExperiment-operate
coerce,	PhosphoExperiment
createFrequencyMat	createFrequencyMat
frequencyScoring	frequencyScoring
GeneSymbol	PhosphoExperiment-methods
GeneSymbol,PhosphoExperiment-method	PhosphoExperiment-methods
GeneSymbol<-	PhosphoExperiment-methods
GeneSymbol<-,PhosphoExperiment-method	PhosphoExperiment-methods
getSPS	getSPS
hSEGs	hSEGs
KinaseFamily	KinaseFamily
kinaseSubstrateHeatmap	kinaseSubstrateHeatmap
kinaseSubstratePred	kinaseSubstratePred
kinaseSubstrateProfile	kinaseSubstrateProfile
kinaseSubstrateScore	kinaseSubstrateScore
Localisation	PhosphoExperiment-methods
Localisation,PhosphoExperiment-method	PhosphoExperiment-methods
Localisation<-	PhosphoExperiment-methods
Localisation<-,PhosphoExperiment-method	PhosphoExperiment-methods
matANOVA	matANOVA
meanAbundance	meanAbundance
medianScaling	medianScaling
minmax	minmax
mIntersect	mIntersect
motif.human.list	motif.human.list
motif.mouse.list	motif.mouse.list
motif.rat.list	motif.rat.list
mSEGs	mSEGs
mUnion	mIntersect
pathwayOverrepresent	pathwayOverrepresent
pathwayRankBasedEnrichment	pathwayRankBasedEnrichment
phosCollapse	phosCollapse
phospho.cells.Ins	phospho.cells.Ins
phospho.cells.Ins.pe	phospho.cells.Ins
phospho.L6.ratio	phospho.L6.ratio
phospho.L6.ratio.pe	phospho.L6.ratio.pe
phospho.liver.Ins.TC.ratio.RUV	phospho.liver.Ins.TC.ratio.RUV
phospho.liver.Ins.TC.ratio.RUV.pe	phospho.liver.Ins.TC.ratio.RUV.pe
PhosphoExperiment	PhosphoExperiment
PhosphoExperiment-class	PhosphoExperiment
PhosphoExperiment-method	PhosphoExperiment
PhosphoSite.human	PhosphoSite.human
PhosphoSite.mouse	PhosphoSite.mouse
PhosphoSite.rat	PhosphoSite.rat
plotKinaseNetwork	plotKinaseNetwork
plotQC	plotQC
plotSignalomeMap	plotSignalomeMap
PPE-accessors	PhosphoExperiment-methods
PPE-operate	PhosphoExperiment-operate
ptImpute	ptImpute
rbind	PhosphoExperiment-operate
rbind,PhosphoExperiment-method	PhosphoExperiment-operate
Residue	PhosphoExperiment-methods
Residue,PhosphoExperiment-method	PhosphoExperiment-methods
Residue<-	PhosphoExperiment-methods
Residue<-,PhosphoExperiment-method	PhosphoExperiment-methods
RUVphospho	RUVphospho
RUVproteome	RUVphospho
scImpute	scImpute
selectGrps	selectGrps
selectLocalisedSites	selectLocalisedSites
selectOverallPercent	selectOverallPercent
selectTimes	selectTimes
Sequence	PhosphoExperiment-methods
Sequence,PhosphoExperiment-method	PhosphoExperiment-methods
Sequence<-	PhosphoExperiment-methods
Sequence<-,PhosphoExperiment-method	PhosphoExperiment-methods
Signalomes	Signalomes
Site	PhosphoExperiment-methods
Site,PhosphoExperiment-method	PhosphoExperiment-methods
Site<-	PhosphoExperiment-methods
Site<-,PhosphoExperiment-method	PhosphoExperiment-methods
siteAnnotate	siteAnnotate
SPSs	SPSs
standardise	standardise
SummarizedExperiment,	PhosphoExperiment
tImpute	tImpute
UniprotID	PhosphoExperiment-methods
UniprotID,PhosphoExperiment-method	PhosphoExperiment-methods
UniprotID<-	PhosphoExperiment-methods
UniprotID<-,PhosphoExperiment-method	PhosphoExperiment-methods
[	PhosphoExperiment-operate
[,PhosphoExperiment,ANY,ANY,ANY-method	PhosphoExperiment-operate
[<-	PhosphoExperiment-operate
[<-,PhosphoExperiment,ANY,ANY,ANY-method	PhosphoExperiment-operate
