Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data R package HaDeX2 version 1.0.0 Processing, analysis and visualization of Hydrogen Deuterium eXchange monitored by Mass Spectrometry experiments (HDX-MS). 'HaDeX2' introduces a new standardized and reproducible workflow for the analysis of the HDX-MS data, including uncertainty propagation, data aggregation and visualization on 3D structure. Additionally, it covers data exploration, quality control and generation of publication-quality figures. All functionalities are also available in the accompanying 'shiny' app. Software Depends: R (>= 3.5) Imports: checkmate, data.table, dplyr, ggplot2, glue, gridExtra, magick, purrr, readr, readxl, r3dmol (>= 0.1.2), remotes, stringi, tidyr, ggiraph Suggests: bookdown, digest, knitr, magrittr, pander, renv, rmarkdown, microbenchmark, testthat, vdiffr, scales, shiny, spelling Weronika Puchala <puchala.weronika@gmail.com> Comprehensive R Archive Network (CRAN) Weronika Puchala [cre, aut] (ORCID: <https://orcid.org/0000-0003-2163-1429>), Michal Burdukiewicz [aut] (ORCID: <https://orcid.org/0000-0001-8926-582X>), Dominik Rafacz [ctb], Krystyna Grzesiak [ctb] GPL-3 2026-02-09 application/tgz https://CRAN.R-project.org/package=HaDeX2 doi:10.32614/CRAN.package.HaDeX2 en-US