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| createFrequencyMat | Create frequency matrix |
| frequencyScoring | Frequency scoring |
| 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 |
| mUnion | Multi-intersection, union |
| pathwayOverrepresent | Gene set over-representation analysis |
| pathwayRankBasedEnrichment | Gene set enrichment analysis |
| Pathways.KEGG | KEGG pathway annotations |
| Pathways.reactome | Reactome pathway annotations |
| phosCollapse | Summarising phosphosites to proteins |
| phospho.cells.Ins | phospho.cells.Ins |
| phospho.L6.ratio | phospho.L6.ratio |
| phospho.liver.Ins.TC.ratio.RUV | phospho_liverInsTC_RUV_sample |
| PhosphoSite.human | PhosphoSitePlus annotations for human |
| PhosphoSite.mouse | PhosphoSitePlus annotations for mouse |
| PhosphoSite.rat | PhosphoSitePlus annotations for rat |
| plotQC | A set of function for data QC plot |
| ptImpute | Paired-tail (pt) based impute |
| RUVphospho | RUV for phosphoproteomics data normalisation |
| RUVproteome | RUV for phosphoproteomics data normalisation |
| scImpute | Site- and condition-specific (sc) impute |
| selectGrps | Select by treatment groups (replicate block) |
| 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 |