This repository contains the source code for SmartPhos package, which provides a one-stop solution for the processing and analysis of mass-spectrometry-based phopho-proteomics data. The package is still under active development. For users with coding experience, they can use the functions provided by SmartPhos to perform data preprocessing, data exploration and analysis. For users without coding experience, SmartPhos also provides a Shiny app called SmartPhos Explorer for the interactive analysis of proteomic and phosphoproteomic data. - [SmartPhos command-line vignette](https://lu-group-ukhd.github.io/SmartPhos/articles/SmartPhos.html) - [SmartPhos Explorer shiny app vignette](https://lu-group-ukhd.github.io/SmartPhos/articles/SmartPhos_Shiny.html)