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

hSEGsStably expression genes in human
matANOVAperform an ANOVA test
meanAbundanceObtain average expression from replicates
medianScalingMedian centering and scaling
mSEGsStably expression genes in mouse
pathwayOverrepresentGene set over-representation analysis
pathwayRankBasedEnrichmentGene set enrichment analysis
Pathways.KEGGKEGG pathway annotations
Pathways.reactomeReactome pathway annotations
phosCollapseSummarising phosphosites to proteins
phosphoESCTime course phosphoproteome of ESC to EpiLC differentiation
PhosphoSite.humanPhosphoSitePlus annotations for human (updated 2019)
PhosphoSite.mousePhosphoSitePlus annotations for mouse (updated 2019)
PhosphoSite.ratPhosphoSitePlus annotations for rat (updated 2019)
plotQCA set of function for data QC plot
ptImputePaired-tail (pt) impute
RUVphosphoRUV for phosphoproteomics data normalisation
RUVproteomeRUV for proteomics data normalisation
selectGrpsSelect by treatment groups (replicate block)
selectOverallPercentSelect phosphosite by percentage of quantification
SPSsStably phosphorylated sites
ssImputeSingle site-based (st) impute
tImputeTail impute
PengyiYang/PhosR documentation built on Dec. 7, 2019, 9:58 a.m.