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Mass spectrometry (MS)-based phosphoproteomics has revolutionised our ability to profile phosphorylation-based signalling in cells and tissues on a global scale. To infer the action of kinases and signalling pathways in phosphoproteomic experiments, we present PhosR, a set of tools and methodologies implemented in a suite of R packages facilitating comprehensive analysis of phosphoproteomic data. By applying PhosR to both published and new phosphoproteomic datasets, we demonstrate capabilitiesdoi:10.1101/2020.08.31.276329 fatcat:3kdd2v43dbbbdn5z4n2g3csrcu