API for PYangLab/PhosR
A set of methods and tools for comprehensive analysis of phosphoproteomics data
| Global functions | |
|---|---|
| .getSignalomes | Source code |
| .kinaseNetwork | Source code |
| .onLoad | Source code |
| .phosRsignalome | Source code |
| .phosphositeClusters | Source code |
| .se_to_pe | Source code |
| GeneSymbol | Man page |
| GeneSymbol,PhosphoExperiment-method | Man page |
| GeneSymbol<- | Man page |
| GeneSymbol<-,PhosphoExperiment-method | Man page |
| KinaseFamily | Man page |
| Localisation | Man page |
| Localisation,PhosphoExperiment-method | Man page |
| Localisation<- | Man page |
| Localisation<-,PhosphoExperiment-method | Man page |
| PPE-accessors | Man page |
| PPE-operate | Man page |
| PhosphoExperiment | Man page Source code |
| PhosphoExperiment-class | Man page |
| PhosphoExperiment-method | Man page |
| PhosphoSite.human | Man page |
| PhosphoSite.mouse | Man page |
| PhosphoSite.rat | Man page |
| RUV | Source code |
| RUVphospho | Man page Source code |
| RUVproteome | Man page Source code |
| Residue | Man page |
| Residue,PhosphoExperiment-method | Man page |
| Residue<- | Man page |
| Residue<-,PhosphoExperiment-method | Man page |
| SPSs | Man page |
| Sequence | Man page |
| Sequence,PhosphoExperiment-method | Man page |
| Sequence<- | Man page |
| Sequence<-,PhosphoExperiment-method | Man page |
| Signalomes | Man page Source code |
| Site | Man page |
| Site,PhosphoExperiment-method | Man page |
| Site<- | Man page |
| Site<-,PhosphoExperiment-method | Man page |
| SummarizedExperiment, | Man page |
| UniprotID | Man page |
| UniprotID,PhosphoExperiment-method | Man page |
| UniprotID<- | Man page |
| UniprotID<-,PhosphoExperiment-method | Man page |
| [ | Man page |
| [,PhosphoExperiment,ANY,ANY,ANY-method | Man page |
| [<- | Man page |
| [<-,PhosphoExperiment,ANY,ANY,ANY-method | Man page |
| abundPlot | Source code |
| annoKinaseSubstrateRelation | Source code |
| cbind | Man page |
| cbind,PhosphoExperiment-method | Man page |
| coerce, | Man page |
| createFrequencyMat | Man page Source code |
| dendPlot | Source code |
| frequencyScoring | Man page Source code |
| generateSignalome | Source code |
| getResidue | Source code |
| getSPS | Man page |
| hSEGs | Man page |
| kinaseActivityHeatmap | Source code |
| kinaseSubstrateHeatmap | Man page Source code |
| kinaseSubstratePred | Man page Source code |
| kinaseSubstrateProfile | Man page Source code |
| kinaseSubstrateScore | Man page Source code |
| mIntersect | Man page Source code |
| mSEGs | Man page |
| mUnion | Man page Source code |
| matANOVA | Man page Source code |
| meanAbundance | Man page Source code |
| medianScale | Source code |
| medianScaling | Man page Source code |
| minmax | Man page Source code |
| motif.human.list | Man page |
| motif.mouse.list | Man page |
| motif.rat.list | Man page |
| multiAdaSampling | Source code |
| pathwayOverrepresent | Man page Source code |
| pathwayRankBasedEnrichment | Man page Source code |
| phosCollapse | Man page Source code |
| phospho.L6.ratio | Man page |
| phospho.L6.ratio.pe | Man page |
| phospho.cells.Ins | Man page |
| phospho.cells.Ins.pe | Man page |
| phospho.liver.Ins.TC.ratio.RUV | Man page |
| phospho.liver.Ins.TC.ratio.RUV.pe | Man page |
| plotKinaseNetwork | Man page Source code |
| plotQC | Man page Source code |
| plotSignalomeMap | Man page Source code |
| ptImpute | Man page Source code |
| quantPlot | Source code |
| rbind | Man page |
| rbind,PhosphoExperiment-method | Man page |
| scImpute | Man page Source code |
| scorePhosphositeProfile | Source code |
| scorePhosphositesMotifs | Source code |
| selectGrps | Man page Source code |
| selectLocalisedSites | Man page Source code |
| selectOverallPercent | Man page Source code |
| selectTimes | Man page Source code |
| siteAnnotate | Man page Source code |
| stImp | Source code |
| standardise | Man page Source code |
| substrateList | Source code |
| tImpute | Man page Source code |
