Package: xcms
Version: 3.99.2
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 = "ctb",
	   comment = c(ORCID = "0000-0002-5022-8009"))
	   )
Depends: R (>= 4.0.0), BiocParallel (>= 1.8.0), MSnbase (>= 2.23.1)
Imports: mzR (>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics
        (>= 1.29.1), lattice, RColorBrewer, plyr, RANN, MassSpecWavelet
        (>= 1.61.3), S4Vectors, robustbase, IRanges,
        SummarizedExperiment, MsCoreUtils (>= 1.11.5), MsFeatures,
        MsExperiment (>= 1.1.2), Spectra (>= 1.9.4), progress, multtest
Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>=
        0.25.1), ncdf4, testthat, pander, rmarkdown, MALDIquant,
        pheatmap, MsBackendMgf, MetaboCoreUtils, signal
Enhances: Rgraphviz, rgl, XML
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: 7.2.3
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' '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-normalization.R'
        'functions-xcmsEIC.R' 'functions-xcmsFragments.R'
        'functions-xcmsRaw.R' 'functions-xcmsSet.R'
        'functions-xcmsSwath.R' 'init.R' 'loadXcmsData.R'
        'matchpeaks.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' 'ramp.R' 'specDist.R'
        'write.mzquantML.R' 'writemzdata.R' 'writemztab.R'
        'xcmsSource.R' 'zzz.R'
git_url: https://git.bioconductor.org/packages/xcms
git_branch: devel
git_last_commit: bf1eb5a
git_last_commit_date: 2023-05-04
Date/Publication: 2023-05-04
NeedsCompilation: yes
Packaged: 2023-05-05 03:55:55 UTC; biocbuild
Author: Colin A. Smith [aut],
  Ralf Tautenhahn [aut],
  Steffen Neumann [aut, cre] (<https://orcid.org/0000-0002-7899-7192>),
  Paul Benton [aut],
  Christopher Conley [aut],
  Johannes Rainer [aut] (<https://orcid.org/0000-0002-6977-7147>),
  Michael Witting [ctb],
  William Kumler [ctb] (<https://orcid.org/0000-0002-5022-8009>)
Maintainer: Steffen Neumann <sneumann@ipb-halle.de>
Built: R 4.3.0; x86_64-w64-mingw32; 2023-05-05 14:39:16 UTC; windows
Archs: x64
