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DESCRIPTION
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DESCRIPTION
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Package: xcms
Version: 4.3.2
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 = "[email protected]",
role = "aut"),
person(given = "Ralf", family = "Tautenhahn",
email = "[email protected]",
role = "aut"),
person(given = "Steffen", family = "Neumann",
email = "[email protected]",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-7899-7192")),
person(given = "Paul", family = "Benton",
email = "[email protected]",
role = "aut"),
person(given = "Christopher", family = "Conley",
email = "[email protected]",
role = "aut"),
person(given = "Johannes", family = "Rainer",
email = "[email protected]",
role = "aut",
comment = c(ORCID = "0000-0002-6977-7147")),
person(given = "Michael", family = "Witting",
email = "[email protected]",
role = "ctb"),
person(given = "William", family = "Kumler",
email = "[email protected]", role = "aut",
comment = c(ORCID = "0000-0002-5022-8009")),
person(given = "Philippine", family = "Louail",
email = "[email protected]",
role = "aut",
comment = c(ORCID = "0009-0007-5429-6846")),
person(given = "Pablo", family = "Vangeenderhuysen",
email = "[email protected]",
role = "ctb",
comment = c(ORCID = "0000-0002-5492-6904")),
person(given = "Carl", family = "Brunius",
email = "[email protected]",
role = "ctb",
comment = c(ORCID = "0000-0003-3957-870X"))
)
Depends:
R (>= 4.0.0),
BiocParallel (>= 1.8.0)
Imports:
MSnbase (>= 2.29.3),
mzR (>= 2.25.3),
methods,
Biobase,
BiocGenerics,
ProtGenerics (>= 1.35.4),
lattice,
MassSpecWavelet (>= 1.66.0),
S4Vectors,
IRanges,
SummarizedExperiment,
MsCoreUtils (>= 1.15.5),
MsFeatures,
MsExperiment (>= 1.5.4),
Spectra (>= 1.13.7),
progress,
RColorBrewer,
MetaboCoreUtils (>= 1.11.2)
Suggests:
BiocStyle,
caTools,
knitr (>= 1.1.0),
faahKO,
msdata (>= 0.25.1),
ncdf4,
testthat (>= 3.1.9),
pander,
rmarkdown,
MALDIquant,
pheatmap,
RANN,
multtest,
MsBackendMgf,
signal,
mgcv
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: 7.3.2
Encoding: UTF-8
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-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'
'ramp.R'
'specDist.R'
'write.mzquantML.R'
'writemzdata.R'
'writemztab.R'
'xcmsSource.R'
'zzz.R'