createFrequencyMat      Create frequency matrix
frequencyScoring        Frequency scoring
getSPS                  Generate set of stable phosphoporylated sites
hSEGs                   A list of Stably Expressed Genes (SEGs)
KinaseFamily            KinaseFamily
kinaseSubstrateHeatmap
                        Kinase-substrate annotation prioritisation
                        heatmap
kinaseSubstratePred     kinaseSubstratePred
kinaseSubstrateProfile
                        Kinase substrate profiling
kinaseSubstrateScore    Kinase substrate scoring
matANOVA                ANOVA test
meanAbundance           Obtain average expression from replicates
medianScaling           Median centering and scaling
minmax                  Minmax scaling
mIntersect              Multi-intersection, union
motif.human.list        List of human kinase motifs
motif.mouse.list        List of mouse kinase motifs
motif.rat.list          List of rat kinase motifs
mSEGs                   A list of Stably Expressed Genes (SEGs)
pathwayOverrepresent    phosphosite/Gene set over-representation
                        analysis
pathwayRankBasedEnrichment
                        Phosphosite/Gene set enrichment analysis
phosCollapse            Summarising phosphosites to proteins
phospho.cells.Ins       phospho.cells.Ins
phospho.L6.ratio        phospho.L6.ratio
phospho.L6.ratio.pe     phospho_L6_ratio_pe
phospho.liver.Ins.TC.ratio.RUV
                        phospho_liverInsTC_RUV_sample
phospho.liver.Ins.TC.ratio.RUV.pe
                        phospho.liver.Ins.TC.ratio.RUV.pe
PhosphoExperiment-class
                        The PhosphoExperiment class
PhosphoSite.human       PhosphoSitePlus annotations for human
PhosphoSite.mouse       PhosphoSitePlus annotations for mouse
PhosphoSite.rat         PhosphoSitePlus annotations for rat
plotKinaseNetwork       Plot kinase network
plotQC                  A set of function for data QC plot
plotSignalomeMap        Plot signalome map
PPE-accessors           PhosphoExperiment object accessors
PPE-operate             PhosphoExperiment object subset, combine
                        methods
ptImpute                Paired-tail (pt) based impute
RUVphospho              RUV for phosphoproteomics data normalisation
scImpute                Site- and condition-specific (sc) impute
selectGrps              Select by treatment groups (replicate block)
selectLocalisedSites    Select phosphosites by localisation score
selectOverallPercent    Select phosphosite by percentage of
                        quantification
selectTimes             selectTimes
Signalomes              PhosR Signalomes
siteAnnotate            Phosphosite annotation
SPSs                    A list of Stably Phosphorylated Sites (SPSs)
standardise             Standardisation
tImpute                 Tail-based impute
