xcms/DESCRIPTION at devel · sneumann/xcms · GitHub

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Package: xcms
Version: 4.11.3
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 (>= 0.59.12),
    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,
    Chromatograms (>= 1.3.3)
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
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/roxygen2/version: 8.1.0