Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data R package HDXBoxeR version 0.0.2 A protocol that facilitates the processing and analysis of Hydrogen-Deuterium Exchange Mass Spectrometry data using p-value statistics and Critical Interval analysis. It provides a pipeline for analyzing data from 'HDXExaminer' (Sierra Analytics, Trajan Scientific), automating matching and comparison of protein states through Welch's T-test and the Critical Interval statistical framework. Additionally, it simplifies data export, generates 'PyMol' scripts, and ensures calculations meet publication standards. 'HDXBoxeR' assists in various aspects of hydrogen-deuterium exchange data analysis, including reprocessing data, calculating parameters, identifying significant peptides, generating plots, and facilitating comparison between protein states. For details check papers by Hageman and Weis (2019) <doi:10.1021/acs.analchem.9b01325> and Masson et al. (2019) <doi:10.1038/s41592-019-0459-y>. 'HDXBoxeR' citation: Janowska et al. (2024) <doi:10.1093/bioinformatics/btae479>. Software Imports: dplyr, graphics, grDevices, RColorBrewer, stats, stringr, tidyr, utils, methods, wrapr Suggests: knitr, rmarkdown, testthat (>= 3.0.0) Maria K. Janowska <mka.janowska@gmail.com> Comprehensive R Archive Network (CRAN) Maria K. Janowska [aut, cre] (ORCID: <https://orcid.org/0000-0002-8232-461X>), Katherine Reiter [ctb], Pearl Magala [ctb], Miklos Guttman [ctb], Rachel E. Klevit [ctb] GPL (>= 2) 2024-08-24 application/tgz https://CRAN.R-project.org/package=HDXBoxeR doi:10.32614/CRAN.package.HDXBoxeR