Package: pmd
Type: Package
Title: Paired Mass Distance Analysis for GC/LC-MS Based Non-Targeted
        Analysis and Reactomics Analysis
Version: 0.3.0
Authors@R: person(given = "Miao", family = "YU",
        role = c("aut", "cre"), 
        email = "yufreecas@gmail.com",
        comment = c(ORCID = "0000-0002-2804-6014"))
Description: Paired mass distance (PMD) analysis proposed in Yu,
        Olkowicz and Pawliszyn (2018) <doi:10.1016/j.aca.2018.10.062>
        and PMD based reactomics analysis proposed in Yu and Petrick
        (2020) <doi:10.1038/s42004-020-00403-z> for gas/liquid
        chromatography–mass spectrometry (GC/LC-MS) based non-targeted
        analysis. PMD analysis including GlobalStd algorithm and
        structure/reaction directed analysis. GlobalStd algorithm could
        found independent peaks in m/z-retention time profiles based on
        retention time hierarchical cluster analysis and frequency
        analysis of paired mass distances within retention time groups.
        Structure directed analysis could be used to find potential
        relationship among those independent peaks in different
        retention time groups based on frequency of paired mass
        distances. Reactomics analysis could also be performed to build
        PMD network, assign sources and make biomarker reaction
        discovery. GUIs for PMD analysis is also included as 'shiny'
        applications.
URL: https://yufree.github.io/pmd/
BugReports: https://github.com/yufree/pmd/issues
License: GPL-2
Encoding: UTF-8
LazyData: true
Suggests: knitr, shiny, rmarkdown
VignetteBuilder: knitr
biocViews:
Depends: R (>= 3.5.0)
Imports: RColorBrewer, stats, graphics, utils, igraph, enviGCMS,
        data.table
RoxygenNote: 7.3.3
Config/pak/sysreqs: libglpk-dev libxml2-dev
Repository: https://yufree.r-universe.dev
Date/Publication: 2026-04-22 13:55:27 UTC
RemoteUrl: https://github.com/yufree/pmd
RemoteRef: HEAD
RemoteSha: 055816392e17674617d6ad563e380f7c91c9a9f1
NeedsCompilation: no
Packaged: 2026-06-21 10:39:11 UTC; root
Author: Miao YU [aut, cre] (ORCID: <https://orcid.org/0000-0002-2804-6014>)
Maintainer: Miao YU <yufreecas@gmail.com>