R (>= 3.1), methods, BiocGenerics (>= 0.7.1), Biobase (>=
2.15.2), mzR (>= 2.13.6), BiocParallel, ProtGenerics (>= 1.9.1)

IRanges (>= 2.13.28), plyr, preprocessCore, vsn, grid, stats4,
affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID (>=
1.5.2), digest, lattice, ggplot2, S4Vectors, 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

Infrastructure, Proteomics, MassSpectrometry,
QualityControl, DataImport

S4 generic functions for Bioconductor proteomics infrastructure

S4 generic functions needed by Bioconductor proteomics
        packages.

parser for netCDF, mzXML, mzData and mzML and mzIdentML files
(mass spectrometry data)

Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer

Steffen Neumann <sneumann@ipb-halle.de>,
Laurent Gatto <lg390@cam.ac.uk>,
Qiang Kou <qkou@umail.iu.edu>

mzR provides a unified API to the common file formats and
        parsers available for mass spectrometry data. It comes with a
        wrapper for the ISB random access parser for mass spectrometry
        mzXML, mzData and mzML files. The package contains the
        original code written by the ISB, and a subset of the
        proteowizard library for mzML and mzIdentML. The netCDF
        reading code has previously been used in XCMS.

Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.9.1)

msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19),
knitr, XML

Infrastructure, DataImport, Proteomics, Metabolomics,
MassSpectrometry

Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou,
 Nathan Russell, Douglas Bates and John Chambers

The 'Rcpp' package provides R functions as well as C++ classes which
 offer a seamless integration of R and C++. Many R data types and objects can be
 mapped back and forth to C++ equivalents which facilitates both writing of new
 code as well as easier integration of third-party libraries. Documentation
 about 'Rcpp' is provided by several vignettes included in this package, via the
 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and
 Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013,
 <doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018,
 <doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details.