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HaDeX2: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

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.

Version: 1.0.0
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
Published: 2026-02-09
DOI: 10.32614/CRAN.package.HaDeX2 (may not be active yet)
Author: Weronika Puchala ORCID iD [cre, aut], Michal Burdukiewicz ORCID iD [aut], Dominik Rafacz [ctb], Krystyna Grzesiak [ctb]
Maintainer: Weronika Puchala <puchala.weronika at gmail.com>
License: GPL-3
URL: https://hadexversum.github.io/HaDeX2/
NeedsCompilation: no
Language: en-US
Materials: README, NEWS, ChangeLog
CRAN checks: HaDeX2 results

Documentation:

Reference manual: HaDeX2.html , HaDeX2.pdf
Vignettes: Importing data (source, R code)
Calculations (source, R code)
Example HDX-MS data analysis (source, R code)
Glossary (source, R code)
Mass calculation (source, R code)
Quality control (source, R code)
Statistics (source, R code)
Data aggregation (source, R code)
Code usage (source, R code)
Comparison between versions (source, R code)
Data visualization (source, R code)

Downloads:

Package source: HaDeX2_1.0.0.tar.gz
Windows binaries: r-devel: not available, r-release: not available, r-oldrel: not available
macOS binaries: r-release (arm64): HaDeX2_1.0.0.tgz, r-oldrel (arm64): HaDeX2_1.0.0.tgz, r-release (x86_64): HaDeX2_1.0.0.tgz, r-oldrel (x86_64): HaDeX2_1.0.0.tgz

Linking:

Please use the canonical form https://CRAN.R-project.org/package=HaDeX2 to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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