Protocol for the processing and downstream analysis of phosphoproteomic data with PhosR
Hani Jieun Kim, Tai-Yun Kim, Di Xiao, Pengyi Yang
Abstract
Analysis of phosphoproteomic data requires advanced computational methodologies. To this end, we developed PhosR, a set of tools and methodologies implemented in R to allow the comprehensive analysis of phosphoproteomic data. PhosR enables processing steps such as imputation, normalization, and functional analysis such as kinase activity inference and signalome construction. Together, PhosR facilitates interpretation and discovery from large-scale phosphoproteomic data sets. For complete details on the use and execution of this protocol, please refer to Kim et al. (2021).
Topics & Concepts
Computer scienceProtocol (science)Normalization (sociology)Database normalizationProfiling (computer programming)InferenceData miningComputational biologyArtificial intelligenceBiologyProgramming languageCluster analysisAlternative medicineMedicineAnthropologyPathologySociologyAdvanced Proteomics Techniques and ApplicationsGene expression and cancer classificationMetabolomics and Mass Spectrometry Studies