Package: MSnbase
Title: Base Functions and Classes for Mass Spectrometry and Proteomics
Version: 2.16.0
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 = "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")))
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 and Lieven
    Clement.
Maintainer: Laurent Gatto <laurent.gatto@uclouvain.be>
Depends: R (>= 3.5), methods, BiocGenerics (>= 0.7.1), Biobase (>=
        2.15.2), mzR (>= 2.19.6), S4Vectors, ProtGenerics (>= 1.19.3)
Imports: BiocParallel, IRanges (>= 2.13.28), plyr, preprocessCore, vsn,
        grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16),
        mzID (>= 1.5.2), digest, lattice, ggplot2, XML, scales, MASS,
        Rcpp
Suggests: testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>=
        1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.7.1), msdata (>=
        0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>=
        2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny, magrittr,
        SummarizedExperiment
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
RoxygenNote: 7.1.1
Collate: 'AllClassUnions.R' 'AllGenerics.R' 'DataClasses.R' 'MzTab.R'
        'NAnnotatedDataFrame.R' 'NTR.R' 'RcppExports.R' 'TMT10.R'
        'TMT11.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-fragments.R'
        'functions-mzR.R' 'functions-plotting.R' 'header.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-ProcessingStep.R'
        'methods-ReporterIons.R' 'methods-Spectrum.R'
        'methods-Spectrum1.R' 'methods-Spectrum2.R'
        'methods-all.equal.R' 'methods-filters.R' 'methods-fragments.R'
        'methods-mzR.R' 'methods-other.R' 'methods-pSet.R'
        'methods-updateObjectTo.R' 'methods-write.R' 'missing-data.R'
        'nadata.R' 'nav.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'
git_url: https://git.bioconductor.org/packages/MSnbase
git_branch: RELEASE_3_12
git_last_commit: bdda714
git_last_commit_date: 2020-10-27
Date/Publication: 2020-10-27
NeedsCompilation: yes
Packaged: 2020-10-28 01:50:26 UTC; biocbuild
Built: R 4.0.3; x86_64-conda-linux-gnu; 2020-10-31 14:31:29 UTC; unix
