R Observatory: Metrics for HaDeX2 version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

HaDeX2

1.0.0

Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data

0packages depend

1.4Kdownloads / year

77.2%test coverage

13/13checks pass

Overview

About

Maintained by Weronika PuchalaFirst published 2026-02-091 releasesCRAN page ↗

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.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)

install.packages("HaDeX2", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-hadex2

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-HaDeX2

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

Slowest check: 13.2 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 1.84

77.2%

Coverage · measured lines

100%

Documentation · exports

15

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 190 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 86%
Documented parameters: 91%
Return-value docs: 100%
References docs: 9%

Downloads

1.4K

CRAN downloads in the past year

Rank #18,817 · ~4/day · ~120/mo

Releases R versions

Daily download trend is not available in this view yet.

14930 days

58090 days

1.4K1 year

Compare downloads with other packages →

Also on56 r2u

Repository

GitHub ↗ hadexversum/hadex2

2Stars

1Forks

1Open issues

0Open PRs

1Releases

1,167Commits

5Contributors

hdx-msmass-spectrometry

1,167 commits · Last activity 2026-02-09

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/hadexversum/hadex2 on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

renv

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

.covrignore

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

28 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (15)

checkmate data.table dplyr ggplot2 glue gridExtra magick purrr readr readxl r3dmol remotes stringi tidyr ggiraph

LinkingTo (0)

none

Suggests (13)

bookdown digest knitr magrittr pander renv rmarkdown microbenchmark testthat vdiffr scales shiny spelling

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Weronika Puchala

Maintainer, Author

Authors (2)

Weronika Puchala

Maintainer, Author

Michal Burdukiewicz

Author

Contributors (2)

Krystyna Grzesiak

Contributor

Dominik Rafacz

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-02-09
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5
Bundled data: 94 KB / 1 file
Download size: 6.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("HaDeX2")

Format

Puchala, W., Burdukiewicz, M., Grzesiak, K., & Rafacz, D. (2026). HaDeX2: Analysis and Visualisation of Hydrogen/Deuterium Exchange Mass Spectrometry Data (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.HaDeX2

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for HaDeX2 version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →