Package: PSMatch
Title: Handling and Managing Peptide Spectrum Matches
Version: 1.17.1
Authors@R: 
   c(person(given = "Laurent", family = "Gatto",
            email = "laurent.gatto@uclouvain.be",
            role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-1520-2268")),
     person(given = "Johannes", family = "Rainer",
            email = "Johannes.Rainer@eurac.edu",
            role = "aut",
            comment = c(ORCID = "0000-0002-6977-7147")),
     person(given = "Sebastian", family = "Gibb",
            email = "mail@sebastiangibb.de",
            role = "aut",
            comment = c(ORCID = "0000-0001-7406-4443")),
     person(given = "Samuel", family = "Wieczorek",
            email = "samuel.wieczorek@cea.fr",
            role = "ctb"),
     person(given = "Thomas", family = "Burger",
            email = "thomas.burger@cea.fr",
            role = "ctb"),
     person(given = "Guillaume", family = "Deflandre",
            email = "guillaume.deflandre@uclouvain.be",
            role = "ctb",
            comment = c(ORCID = "0009-0008-1257-2416")))
Description: The PSMatch package helps proteomics practitioners to
        load, handle and manage Peptide Spectrum Matches. It provides
        functions to model peptide-protein relations as adjacency
        matrices and connected components, visualise these as graphs
        and make informed decision about shared peptide filtering. The
        package also provides functions to calculate and visualise MS2
        fragment ions.
Depends: S4Vectors, R (>= 4.1.0), PTMods (>= 0.99.4)
Imports: utils, stats, igraph, methods, Spectra (>= 1.17.10), Matrix,
        BiocParallel, BiocGenerics, ProtGenerics (>= 1.27.1),
        QFeatures, MsCoreUtils
Suggests: MsDataHub, rpx, mzID, mzR, SummarizedExperiment, BiocStyle,
        rmarkdown, knitr, factoextra, vdiffr (>= 1.0.0), testthat
License: Artistic-2.0
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
BugReports: https://github.com/RforMassSpectrometry/PSM/issues
URL: https://github.com/RforMassSpectrometry/PSM
biocViews: Infrastructure, Proteomics, MassSpectrometry
Config/roxygen2/version: 8.0.0
RoxygenNote: 7.3.3
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libuv1-dev
        libxml2-dev libssl-dev zlib1g-dev
Repository: https://rformassspectrometry.r-universe.dev
Date/Publication: 2026-05-20 15:56:30 UTC
RemoteUrl: https://github.com/rformassspectrometry/psmatch
RemoteRef: HEAD
RemoteSha: ff1b83c66e28c7c6e93c55ee456ad92772ba2afb
NeedsCompilation: no
Packaged: 2026-07-23 11:11:13 UTC; root
Author: Laurent Gatto [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-1520-2268>),
  Johannes Rainer [aut] (ORCID: <https://orcid.org/0000-0002-6977-7147>),
  Sebastian Gibb [aut] (ORCID: <https://orcid.org/0000-0001-7406-4443>),
  Samuel Wieczorek [ctb],
  Thomas Burger [ctb],
  Guillaume Deflandre [ctb] (ORCID:
    <https://orcid.org/0009-0008-1257-2416>)
Maintainer: Laurent Gatto <laurent.gatto@uclouvain.be>