BiocParallel, IRanges (>= 2.13.28), plyr, preprocessCore, vsn,
grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16),
mzID (>= 1.5.2), digest, lattice, ggplot2, XML, scales, MASS,
Rcpp

testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>=
1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.7.1), msdata (>=
0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>=
2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny, magrittr,
SummarizedExperiment

ImmunoOncology, Infrastructure, Proteomics,
MassSpectrometry, QualityControl, DataImport

'AllClassUnions.R' 'AllGenerics.R' 'DataClasses.R' 'MzTab.R'
'NTR.R' 'RcppExports.R' 'TMT10.R' 'TMT11.R' 'TMT6.R' 'TMT7.R'
'averageMSnSet.R' 'cache.R' 'coerce.R' 'combineFeatures.R'
'compfnames.R' 'environment.R' 'fData-utils.R'
'fdata-selection.R' 'foi.R' 'functions-Chromatogram.R'
'functions-Chromatograms.R' 'functions-MIAPE.R'
'functions-MSnExp.R' 'functions-MSnProcess.R'
'functions-MSnSet.R' 'functions-OnDiskMSnExp.R'
'functions-ReporterIons.R' 'functions-Spectra.R'
'functions-Spectrum.R' 'functions-Spectrum1.R'
'functions-Spectrum2.R' 'functions-addIdentificationData.R'
'functions-fragments.R' 'functions-mzR.R'
'functions-plotting.R' 'header.R' 'hmap.R' 'iPQF.R' 'iTRAQ4.R'
'iTRAQ5.R' 'iTRAQ8.R' 'iTRAQ9.R' 'imputation.R' 'map.R'
'matching.R' 'methods-Chromatogram.R' 'methods-Chromatograms.R'
'methods-MIAPE.R' 'methods-MSnExp.R' 'methods-MSnProcess.R'
'methods-MSnSet.R' 'methods-MSnSetList.R'
'methods-NAnnotatedDataFrame.R' 'methods-OnDiskMSnExp.R'
'methods-ProcessingStep.R' 'methods-ReporterIons.R'
'methods-Spectra.R' 'methods-Spectrum.R' 'methods-Spectrum1.R'
'methods-Spectrum2.R' 'methods-all.equal.R' 'methods-filters.R'
'methods-fragments.R' 'methods-mzR.R' 'methods-other.R'
'methods-pSet.R' 'methods-updateObjectTo.R' 'methods-write.R'
'missing-data.R' 'nadata.R' 'nav.R' 'options.R'
'plotting-MSnExp.R' 'plotting-MSnSet.R'
'plotting-OnDiskMSnExp.R' 'plotting-Spectrum.R'
'plotting-Spectrum1.R' 'plotting-Spectrum2.R'
'plotting-dataframe.R' 'quantitation-MS2-isobaric.R'
'quantitation-MS2-labelfree.R' 'readChromData.R' 'readMSData.R'
'readMSData2.R' 'readMSnSet.R' 'readMzXMLData.R'
'readWriteMgfData.R' 'readWriteMzTab.R' 'utils.R'
'writeMSData.R' 'zzz.R'