R Observatory: Metrics for HDXBoxeR version 0.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

HDXBoxeR

0.0.2Package record

Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data

0packages depend

2.3Kdownloads / year

–test coverage

8/13flavors OK

Overview

About

Maintained by Maria K. JanowskaCRAN page ↗

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.

Install

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

install.packages("HDXBoxeR", 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-hdxboxer

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-HDXBoxeR

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

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

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-HDXBoxeR

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

5NOTE8OK

Check messages

NOTER code for possible problemsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Found calls to structure() using deprecated special names:
  HDXBoxeR/R/ppar.R (.Names: 1)
'.Names' should be changed to 'names'.

CRAN check page ↗

Slowest check: 3.1 min · r-oldrel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE10 OK, 3 NOTE2026-07-16
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.0.2

READMEYes · 315 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 112
Examples that run: 79%52 run in a plain check · 14 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 59%
Documented parameters: 92%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

HDXBoxeR

How these are measured

Downloads

2.3K

CRAN downloads in the past year

Rank #19,700 · ~6/day · ~189/mo

Releases R versions

Daily download trend is not available in this view yet.

22930 days

67590 days

2.3K1 year

Compare downloads with other packages →

Also on74 r2u5 autocran

How downloads are counted

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing HDXBoxeR adds 22 packages (12 with compiled code, 18 MB of source tarballs). Heaviest: stringi 11 MB, vctrs 1.0 MB, dplyr 902 KB.

Depends (0)

none

Imports (10)

dplyrgraphicsgrDevicesRColorBrewerstatsstringr tidyrutilsmethodswrapr

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (5)

Maria K. Janowska

Author, Maintainer since 0.0.1 (2024)

Contributor

Contributor

Contributor

Contributor

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.0.2Latest
record
2024-08-24 · current release · diff ↗ ·
added 1 export
nb_exch_deut
R
R 4.4.0 released · 2024-04-24
0.0.1
record
2024-04-10
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-04-10
Total releases: 2 / 2 yrs
License: GPL (>= 2) OSI
Download size: 1.0 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("HDXBoxeR")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/bioinformatics/btae479.

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 HDXBoxeR version 0.0.2 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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