Package: MSnbase
Title: Base Functions and Classes for Mass Spectrometry and Proteomics
Version: 2.37.0
Description: MSnbase provides infrastructure for manipulation,
             processing and visualisation of mass spectrometry and
             proteomics data, ranging from raw to quantitative and
             annotated data.
Authors@R: c(person(given = "Laurent", family = "Gatto",
                    email = "laurent.gatto@uclouvain.be",
                    comment = c(ORCID = "0000-0002-1520-2268"),
                    role = c("aut","cre")),
             person(given = "Guangchuang", family = "Yu",
                    email = "guangchuangyu@gmail.com",
                    role = "ctb"),
             person(given = "Samuel", family = "Wieczorek",
                    email = "samuel.wieczorek@cea.fr",
                    role = "ctb"),
             person(given = "Vasile-Cosmin", family = "Lazar",
                    email = "v.cosmin.lazar@googlemail.com",
                    role = "ctb"),
             person(given = "Vladislav", family = "Petyuk",
                    email = "petyuk@gmail.com",
                    role = "ctb"),
             person(given = "Thomas", family = "Naake",
                    email = "tn299@cam.ac.uk",
                    role = "ctb"),
             person(given = "Richie", family = "Cotton",
                    email = "richierocks@gmail.com",
                    role = "ctb"),
             person(given = "Steffen", family = "Neumann",
                    email = "sneumann@ipb-halle.de",
                    role = "ctb"),
             person(given = "Arne", family = "Smits",
                    email = "arne.smits@embl.de",
                    role = "ctb"),
             person(given = "Martina", family = "Fischer",
                    email = "FischerM@rki.de",
                    role = "ctb"),
             person(given = "Adriaan", family = "Sticker",
                    email = "adriaan.sticker@ugent.be",
                    role = "ctb"),
             person(given = "Ludger", family = "Goeminne",
                    email = " ludger.goeminne@vib-ugent.be",
                    role = "ctb"),
             person(given = "Lieven", family = "Clement",
                    email = "Lieven.Clement@ugent.be",
                    role = "ctb"),
             person(given = "Sigurdur", family = "Smarason",
                    email = " Sigurdur.Smarason@eurac.edu",
                    role = "ctb"),
             person(given = "Miguel", family = "Cosenza-Contreras",
                    email = "migueljcc5@gmail.com",
                    role = "ctb"),
             person(given = "Pascal", family = "Maas",
                    email = "p.maas@lacdr.leidenuniv.nl",
                    comment = c(ORCID = "0000-0001-9379-6041"),
                    role = "ctb"),
             person(given = "Johannes", family = "Rainer",
                    email = "Johannes.Rainer@eurac.edu",
                    role = c("aut", "cre"),
                    comment = c(ORCID = "0000-0002-6977-7147")),
             person(given = "Sebastian", family = "Gibb",
                    email = "mail@sebastiangibb.de",
                    role = c("aut", "cre"),
                    comment=c(ORCID="0000-0001-7406-4443")))
Author: Laurent Gatto, Johannes Rainer and Sebastian Gibb with
    contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin
    Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits,
    Martina Fisher, Ludger Goeminne, Adriaan Sticker, Lieven
    Clement and Pascal Maas.
Maintainer: Laurent Gatto <laurent.gatto@uclouvain.be>
Depends:
    R (>= 3.5),
    methods,
    BiocGenerics (>= 0.7.1),
    Biobase (>= 2.15.2),
    mzR (>= 2.29.3),
    S4Vectors,
    ProtGenerics (>= 1.29.1)
Imports:
    MsCoreUtils,
    PSMatch (>= 1.13.2),
    BiocParallel,
    IRanges (>= 2.13.28),
    plyr,
    vsn,
    grid,
    stats4,
    affy,
    impute,
    pcaMethods,
    MALDIquant (>= 1.16),
    mzID (>= 1.5.2),
    digest,
    lattice,
    ggplot2,
    scales,
    MASS,
    Rcpp
Suggests:
    testthat,
    pryr,
    gridExtra,
    microbenchmark,
    zoo,
    knitr (>= 1.1.0),
    rols,
    Rdisop,
    pRoloc,
    pRolocdata (>= 1.43.3),
    magick,
    msdata (>= 0.19.3),
    roxygen2,
    rgl,
    rpx,
    AnnotationHub,
    BiocStyle (>= 2.5.19),
    rmarkdown,
    imputeLCMD,
    norm,
    gplots,
    XML,
    shiny,
    magrittr,
    SummarizedExperiment,
    Spectra
LinkingTo: Rcpp
License: Artistic-2.0
LazyData: yes
VignetteBuilder: knitr
Encoding: UTF-8
BugReports: https://github.com/lgatto/MSnbase/issues
URL: https://lgatto.github.io/MSnbase
biocViews: ImmunoOncology, Infrastructure, Proteomics, MassSpectrometry,
    QualityControl, DataImport
Roxygen: list(markdown=TRUE)
Collate:
    'AllClassUnions.R'
    'AllGenerics.R'
    'DataClasses.R'
    'MzTab.R'
    'NTR.R'
    'RcppExports.R'
    'TMT10.R'
    'TMT11.R'
    'TMT16.R'
    'TMT6.R'
    'TMT7.R'
    'averageMSnSet.R'
    'cache.R'
    'coerce.R'
    'combineFeatures.R'
    'compfnames.R'
    'environment.R'
    'fData-utils.R'
    'fdata-selection.R'
    'foi.R'
    'functions-Chromatogram.R'
    'functions-MChromatograms.R'
    'functions-MIAPE.R'
    'functions-MSnExp.R'
    'functions-MSnProcess.R'
    'functions-MSnSet.R'
    'functions-MSpectra.R'
    'functions-OnDiskMSnExp.R'
    'functions-ReporterIons.R'
    'functions-Spectrum.R'
    'functions-Spectrum1.R'
    'functions-Spectrum2.R'
    'functions-addIdentificationData.R'
    'functions-mzR.R'
    'functions-plotting.R'
    'hmap.R'
    'iPQF.R'
    'iTRAQ4.R'
    'iTRAQ5.R'
    'iTRAQ8.R'
    'iTRAQ9.R'
    'imputation.R'
    'map.R'
    'matching.R'
    'methods-Chromatogram.R'
    'methods-MChromatograms.R'
    'methods-MIAPE.R'
    'methods-MSnExp.R'
    'methods-MSnProcess.R'
    'methods-MSnSet.R'
    'methods-MSnSetList.R'
    'methods-MSpectra.R'
    'methods-OnDiskMSnExp.R'
    'methods-ReporterIons.R'
    'methods-Spectrum.R'
    'methods-Spectrum1.R'
    'methods-Spectrum2.R'
    'methods-all.equal.R'
    'methods-filters.R'
    'methods-mzR.R'
    'methods-other.R'
    'methods-pSet.R'
    'methods-updateObjectTo.R'
    'methods-write.R'
    'missing-data.R'
    'nadata.R'
    'options.R'
    'plotting-MSnExp.R'
    'plotting-MSnSet.R'
    'plotting-Spectrum.R'
    'plotting-Spectrum1.R'
    'plotting-Spectrum2.R'
    'plotting-dataframe.R'
    'quantitation-MS2-isobaric.R'
    'quantitation-MS2-labelfree.R'
    'readChromData.R'
    'readMSData.R'
    'readMSData2.R'
    'readMSnSet.R'
    'readMzXMLData.R'
    'readWriteMgfData.R'
    'readWriteMzTab.R'
    'utils.R'
    'writeMSData.R'
    'zzz.R'
RoxygenNote: 7.3.2
git_url: https://git.bioconductor.org/packages/MSnbase
git_branch: devel
git_last_commit: 3ca1ea4
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
