methods, xcms, RBGL, graph, graphics, grDevices, stats, utils,
Hmisc, igraph

Annotation of peaklists generated by xcms, rule based annotation
    of isotopes and adducts, isotope validation, EIC correlation based tagging of
    unknown adducts and fragments

Colin A. Smith <csmith@scripps.edu>,
    Ralf Tautenhahn <rtautenh@gmail.com>,
    Steffen Neumann <sneumann@ipb-halle.de>,
    Paul Benton <hpbenton@scripps.edu>,
    Christopher Conley <cjconley@ucdavis.edu>,
    Johannes Rainer <Johannes.Rainer@eurac.edu>

R (>= 2.14.0),
methods,
Biobase,
BiocParallel (>= 1.8.0),
MSnbase (>= 2.5.10)

mzR (>= 2.13.1),
BiocGenerics,
ProtGenerics,
lattice,
RColorBrewer,
plyr,
RANN,
multtest,
MassSpecWavelet (>= 1.5.2),
S4Vectors,
robustbase

BiocStyle,
caTools,
knitr (>= 1.1.0),
faahKO,
msdata,
ncdf4,
rgl,
microbenchmark,
testthat,
pander,
magrittr,
MALDIquant

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.

'AllGenerics.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-utils.R'
'functions-IO.R'
'functions-OnDiskMSnExp.R'
'functions-ProcessHistory.R'
'functions-XCMSnExp.R'
'functions-normalization.R'
'functions-xcmsEIC.R'
'functions-xcmsFragments.R'
'functions-xcmsRaw.R'
'functions-xcmsSet.R'
'init.R'
'matchpeaks.R'
'methods-Chromatogram.R'
'methods-IO.R'
'methods-MsFeatureData.R'
'methods-OnDiskMSnExp.R'
'methods-Params.R'
'methods-ProcessHistory.R'
'methods-XCMSnExp.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'