Collection of annotation related methods for mass spectrometry
data

Carsten Kuhl, Ralf Tautenhahn, Hendrik Treutler, Steffen Neumann {ckuhl|htreutle|sneumann}@ipb-halle.de, rtautenh@scripps.edu

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 (>= 2.7.8)

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-imputation.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'