Package: xcms
Version: 4.11.0
Title: LC-MS and GC-MS Data Analysis
Description: Framework for processing and visualization of
        chromatographically separated and single-spectra mass spectral
        data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML
        files. Preprocesses data for high-throughput, untargeted
        analyte profiling.
Authors@R: c(
	   person(given = "Colin A.", family = "Smith",
	   email = "csmith@scripps.edu",
	   role = "aut"),
	   person(given = "Ralf", family = "Tautenhahn",
	   email = "rtautenh@gmail.com",
	   role = "aut"),
	   person(given = "Steffen", family = "Neumann",
	   email = "sneumann@ipb-halle.de",
	   role = c("aut", "cre"),
	   comment = c(ORCID = "0000-0002-7899-7192")),
	   person(given = "Paul", family = "Benton",
	   email = "hpbenton@scripps.edu",
	   role = "aut"),
	   person(given = "Christopher", family = "Conley",
	   email = "cjconley@ucdavis.edu",
	   role = "aut"),
	   person(given = "Johannes", family = "Rainer",
	   email = "johannes.rainer@eurac.edu",
	   role = "aut",
	   comment = c(ORCID = "0000-0002-6977-7147")),
	   person(given = "Michael", family = "Witting",
	   email = "michael.witting@helmholtz-muenchen.de",
	   role = "ctb"),
	   person(given = "William", family = "Kumler",
	   email = "wkumler@uw.edu", role = "aut",
	   comment = c(ORCID = "0000-0002-5022-8009")),
	   person(given = "Philippine", family = "Louail",
	   email = "philippine.louail@eurac.edu",
	   role = "aut",
	   comment = c(ORCID = "0009-0007-5429-6846")),
	   person(given = "Pablo", family = "Vangeenderhuysen",
	   email = "pablo.vangeenderhuysen@ugent.be",
	   role = "ctb",
	   comment = c(ORCID = "0000-0002-5492-6904")),
	   person(given = "Carl", family = "Brunius",
	   email = "carl.brunius@chalmers.se",
	   role = "ctb",
	   comment = c(ORCID = "0000-0003-3957-870X"))
	   )
Depends: R (>= 4.1.0), BiocParallel (>= 1.8.0)
Imports: MSnbase (>= 2.33.3), mzR (>= 2.25.3), methods, Biobase,
        BiocGenerics, ProtGenerics (>= 1.37.1), lattice,
        MassSpecWavelet (>= 1.66.0), S4Vectors, IRanges,
        SummarizedExperiment, MsCoreUtils (>= 1.19.2), MsFeatures,
        MsExperiment (>= 1.5.4), Spectra (>= 1.21.5), progress,
        RColorBrewer, MetaboCoreUtils (>= 1.11.2), data.table
Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, ncdf4, testthat
        (>= 3.1.9), pander, rmarkdown, MALDIquant, pheatmap, RANN,
        multtest, MsBackendMgf, signal, mgcv, rhdf5, MsDataHub (>=
        1.11.2)
Enhances: Rgraphviz, rgl
License: GPL (>= 2) + file LICENSE
URL: https://github.com/sneumann/xcms
BugReports: https://github.com/sneumann/xcms/issues/new
VignetteBuilder: knitr
biocViews: ImmunoOncology, MassSpectrometry, Metabolomics
RoxygenNote: 7.3.3
Encoding: UTF-8
Roxygen: list(markdown=TRUE)
Collate: 'AllGenerics.R' 'functions-XChromatograms.R'
        'functions-XChromatogram.R' 'DataClasses.R' 'Deprecated.R'
        'MPI.R' 'MsExperiment-functions.R' 'MsExperiment.R'
        'XcmsExperiment-functions.R' 'XcmsExperiment-plotting.R'
        'XcmsExperiment.R' 'XcmsExperimentHdf5-functions.R'
        'hidden_aliases.R' 'XcmsExperimentHdf5.R' 'c.R' 'cwTools.R'
        'databases.R' 'functions-MsFeatureData.R'
        'do_adjustRtime-functions.R' 'functions-binning.R'
        'do_findChromPeaks-functions.R' 'functions-Params.R'
        'do_groupChromPeaks-functions.R' 'fastMatch.R'
        'functions-Chromatogram.R' 'functions-utils.R' 'functions-IO.R'
        'functions-OnDiskMSnExp.R' 'functions-ProcessHistory.R'
        'functions-XCMSnExp.R' 'functions-imputation.R'
        'functions-xcmsEIC.R' 'functions-xcmsFragments.R'
        'functions-xcmsRaw.R' 'functions-xcmsSet.R'
        'functions-xcmsSwath.R' 'init.R' 'loadXcmsData.R'
        'matchpeaks.R' 'method-filterFeatures.R'
        'methods-Chromatogram.R' 'methods-IO.R'
        'methods-MChromatograms.R' 'methods-MsFeatureData.R'
        'methods-OnDiskMSnExp.R' 'methods-Params.R'
        'methods-ProcessHistory.R' 'methods-XCMSnExp.R'
        'methods-XChromatogram.R' 'methods-XChromatograms.R'
        'methods-group-features.R' 'methods-xcmsEIC.R'
        'methods-xcmsFileSource.R' 'methods-xcmsFragments.R'
        'methods-xcmsPeaks.R' 'methods-xcmsRaw.R' 'methods-xcmsSet.R'
        'models.R' 'mzClust.R' 'plotQC.R' 'specDist.R'
        'write.mzquantML.R' 'writemzdata.R' 'writemztab.R'
        'xcmsSource.R' 'zzz.R'
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: 2026-04-28 12:31:04 UTC
RemoteUrl: https://github.com/bioc/xcms
RemoteRef: HEAD
RemoteSha: efc4813585b725fe50ac20676c95f0db10c7445e
NeedsCompilation: yes
Packaged: 2026-06-23 15:35:18 UTC; root
Author: Colin A. Smith [aut],
  Ralf Tautenhahn [aut],
  Steffen Neumann [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-7899-7192>),
  Paul Benton [aut],
  Christopher Conley [aut],
  Johannes Rainer [aut] (ORCID: <https://orcid.org/0000-0002-6977-7147>),
  Michael Witting [ctb],
  William Kumler [aut] (ORCID: <https://orcid.org/0000-0002-5022-8009>),
  Philippine Louail [aut] (ORCID:
    <https://orcid.org/0009-0007-5429-6846>),
  Pablo Vangeenderhuysen [ctb] (ORCID:
    <https://orcid.org/0000-0002-5492-6904>),
  Carl Brunius [ctb] (ORCID: <https://orcid.org/0000-0003-3957-870X>)
Maintainer: Steffen Neumann <sneumann@ipb-halle.de>