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
RoxygenNote: 7.2.3
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2024-08-23 19:16:44 UTC; mkaja
Repository: CRAN
Date/Publication: 2024-08-24 07:30:10 UTC
Built: R 4.4.3; ; 2025-12-29 19:21:24 UTC; windows
