Package: MSnbase Title: Base Functions and Classes for Mass Spectrometry and Proteomics Version: 2.39.1 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 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 (>= 1.15.3), PTMods (>= 0.99.5), 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, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), Rdisop, pRoloc, pRolocdata (>= 1.43.3), magick, MsDataHub, msdata, 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' Config/roxygen2/version: 8.0.0 Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libuv1-dev libxml2-dev libnetcdf-dev libssl-dev zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-05-04 18:40:43 UTC RemoteUrl: https://github.com/bioc/MSnbase RemoteRef: HEAD RemoteSha: 76555a2e5da6d8087f2a3a208c03faf8dca5449a NeedsCompilation: yes Packaged: 2026-06-23 15:26:22 UTC; root