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DESCRIPTION
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DESCRIPTION
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Package: xcms
Version: 3.9.2
Title: LC-MS and GC-MS Data Analysis
Authors@R: c(
person(given = "Colin A.", family = "Smith",
email = "[email protected]",
role = "ctb"),
person(given = "Ralf", family = "Tautenhahn",
email = "[email protected]",
role = "ctb"),
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 = "ctb"),
person(given = "Christopher", family = "Conley",
email = "[email protected]",
role = "ctb"),
person(given = "Johannes", family = "Rainer",
email = "[email protected]",
role = "ctb",
comment = c(ORCID = "0000-0002-6977-7147")),
person(given = "Michael", family = "Witting",
email = "[email protected]",
role = "ctb")
)
Author: Colin A. Smith <[email protected]>,
Ralf Tautenhahn <[email protected]>,
Steffen Neumann <[email protected]>,
Paul Benton <[email protected]>,
Christopher Conley <[email protected]>,
Johannes Rainer <[email protected]>,
Michael Witting <[email protected]>
Maintainer: Steffen Neumann <[email protected]>
Depends:
R (>= 2.14.0),
methods,
Biobase,
BiocParallel (>= 1.8.0),
MSnbase (>= 2.9.3)
Imports:
mzR (>= 2.19.5),
BiocGenerics,
ProtGenerics (>= 1.17.2),
lattice,
RColorBrewer,
plyr,
RANN,
multtest,
MassSpecWavelet (>= 1.5.2),
S4Vectors,
robustbase,
IRanges
Suggests:
BiocStyle,
caTools,
knitr (>= 1.1.0),
faahKO,
msdata (>= 0.25.1),
ncdf4,
rgl,
microbenchmark,
testthat,
pander,
magrittr,
MALDIquant,
pheatmap
Enhances:
Rgraphviz,
Rmpi,
XML
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.
License: GPL (>= 2) + file LICENSE
URL: https://github.com/sneumann/xcms
VignetteBuilder: knitr
BugReports: https://github.com/sneumann/xcms/issues/new
biocViews: ImmunoOncology, MassSpectrometry, Metabolomics
RoxygenNote: 7.0.2
Collate:
'AllGenerics.R'
'functions-XChromatograms.R'
'functions-XChromatogram.R'
'DataClasses.R'
'Deprecated.R'
'MPI.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'
'matchpeaks.R'
'methods-Chromatogram.R'
'methods-Chromatograms.R'
'methods-IO.R'
'methods-MsFeatureData.R'
'methods-OnDiskMSnExp.R'
'methods-Params.R'
'methods-ProcessHistory.R'
'methods-XCMSnExp.R'
'methods-XChromatogram.R'
'methods-XChromatograms.R'
'methods-xcmsEIC.R'
'methods-xcmsFileSource.R'
'methods-xcmsFragments.R'
'methods-xcmsPeaks.R'
'methods-xcmsRaw.R'
'methods-xcmsSet.R'
'models.R'
'mzClust.R'
'netCDF.R'
'plotQC.R'
'ramp.R'
'specDist.R'
'write.mzquantML.R'
'writemzdata.R'
'writemztab.R'
'xcmsSource.R'
'zzz.R'