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HDXBoxeR: Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data

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>.

Version: 0.0.2
Imports: dplyr, graphics, grDevices, RColorBrewer, stats, stringr, tidyr, utils, methods, wrapr
Suggests: knitr, rmarkdown, testthat (≥ 3.0.0)
Published: 2024-08-24
DOI: 10.32614/CRAN.package.HDXBoxeR
Author: Maria K. Janowska ORCID iD [aut, cre], Katherine Reiter [ctb], Pearl Magala [ctb], Miklos Guttman [ctb], Rachel E. Klevit [ctb]
Maintainer: Maria K. Janowska <mka.janowska at gmail.com>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
Citation: HDXBoxeR citation info
Materials: README
CRAN checks: HDXBoxeR results

Documentation:

Reference manual: HDXBoxeR.pdf
Vignettes: HDXBoxeR (source, R code)

Downloads:

Package source: HDXBoxeR_0.0.2.tar.gz
Windows binaries: r-devel: HDXBoxeR_0.0.2.zip, r-release: HDXBoxeR_0.0.2.zip, r-oldrel: HDXBoxeR_0.0.2.zip
macOS binaries: r-release (arm64): HDXBoxeR_0.0.2.tgz, r-oldrel (arm64): HDXBoxeR_0.0.2.tgz, r-release (x86_64): HDXBoxeR_0.0.2.tgz, r-oldrel (x86_64): HDXBoxeR_0.0.2.tgz
Old sources: HDXBoxeR archive

Linking:

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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.