Man pages for PengyiYang/PhosR
A set of methods and tools for comprehensive analysis of phosphoproteomics data

createFrequencyMatCreate frequency matrix
frequencyScoringFrequency scoring
KinaseFamilyKinaseFamily
kinaseSubstrateHeatmapKinase-substrate annotation prioritisation heatmap
kinaseSubstratePredkinaseSubstratePred
kinaseSubstrateProfileKinase substrate profiling
kinaseSubstrateScoreKinase substrate scoring
matANOVAANOVA test
meanAbundanceObtain average expression from replicates
medianScalingMedian centering and scaling
minmaxMinmax scaling
mIntersectMulti-intersection, union
motif.human.listList of human kinase motifs
motif.mouse.listList of mouse kinase motifs
motif.rat.listList of rat kinase motifs
pathwayOverrepresentGene set over-representation analysis
pathwayRankBasedEnrichmentGene set enrichment analysis
Pathways.KEGGKEGG pathway annotations
Pathways.reactomeReactome pathway annotations
phosCollapseSummarising phosphosites to proteins
phospho.cells.Insphospho.cells.Ins
phospho.L6.ratiophospho.L6.ratio
phospho.liver.Ins.TC.ratio.RUVphospho_liverInsTC_RUV_sample
PhosphoSite.humanPhosphoSitePlus annotations for human
PhosphoSite.mousePhosphoSitePlus annotations for mouse
PhosphoSite.ratPhosphoSitePlus annotations for rat
plotQCA set of function for data QC plot
ptImputePaired-tail (pt) based impute
RUVphosphoRUV for phosphoproteomics data normalisation
scImputeSite- and condition-specific (sc) impute
selectGrpsSelect by treatment groups (replicate block)
selectOverallPercentSelect phosphosite by percentage of quantification
selectTimesselectTimes
SignalomesPhosR Signalomes
siteAnnotatePhosphosite annotation
SPSsA list of Stably Phosphorylated Sites (SPSs)
standardiseStandardisation
tImputeTail-based impute
PengyiYang/PhosR documentation built on June 21, 2020, 8:37 a.m.