Type: Package
Package: HDXBoxeR
Title: Analysis of Hydrogen-Deuterium Exchange Mass-Spectrometry Data
Version: 0.0.2
Authors@R: c(person("Maria K.", "Janowska", role = c("aut", "cre"), 
            email="mka.janowska@gmail.com",
           comment = c(ORCID = "0000-0002-8232-461X")),
             person("Katherine", "Reiter", role = "ctb"),
             person("Pearl", "Magala", role = "ctb"),
             person("Miklos", "Guttman", role = "ctb"),
             person("Rachel E.", "Klevit", role = "ctb"))
Author: Maria K. Janowska [aut, cre]
        (<https://orcid.org/0000-0002-8232-461X>), Katherine Reiter
        [ctb], Pearl Magala [ctb], Miklos Guttman [ctb], Rachel E.
        Klevit [ctb]
Maintainer: Maria K. Janowska <mka.janowska@gmail.com>
Description: 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>.
License: GPL (>= 2)
Imports: dplyr, graphics, grDevices, RColorBrewer, stats, stringr,
        tidyr, utils, methods, wrapr
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)
VignetteBuilder: knitr, rmarkdown
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Config/testthat/edition: 3
Config/pak/sysreqs: libicu-dev
Repository: https://mkajano.r-universe.dev
Date/Publication: 2024-08-14 06:12:11 UTC
RemoteUrl: https://github.com/mkajano/hdxboxer
RemoteRef: HEAD
RemoteSha: 63fdd47db29cfc589237ff67350de3aea76ea540
NeedsCompilation: no
Packaged: 2026-10-03 07:24:23 UTC; root