To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("mzR")

In most cases, you don't need to download the package archive at all.

mzR

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see mzR.

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

Bioconductor version: 3.1

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.

Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou

Maintainer: Bernd Fischer <b.fischer at dkfz.de>, Steffen Neumann <sneumann at ipb-halle.de>, Laurent Gatto <lg390 at cam.ac.uk>, Qiang Kou <qkou at umail.iu.edu>

Citation (from within R, enter citation("mzR")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("mzR")

Documentation

To view documentation for the version of this package installed in your system, start R and enter: 

browseVignettes("mzR")
PDF R Script Accessin raw mass spectrometry and identification data
PDF Reference Manual
Text NEWS

Details

biocViews DataImport, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version 2.2.2
In Bioconductor since BioC 2.9 (R-2.14) (4.5 years)
License Artistic-2.0
Depends Rcpp (>= 0.10.1), methods, utils
Imports Biobase, BiocGenerics(>= 0.13.6), ProtGenerics
LinkingTo Rcpp, zlibbioc
Suggests msdata(>= 0.3.5), RUnit, mzID, BiocStyle, knitr
SystemRequirements GNU make, NetCDF
Enhances
URL https://github.com/sneumann/mzR/
BugReports https://github.com/sneumann/mzR/issues/new
Depends On Me MSGFgui, MSnbase, TargetSearch, xcms
Imports Me Pbase, RMassBank, SIMAT
Suggests Me qcmetrics, RforProteomics
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source mzR_2.2.2.tar.gz
Windows Binary mzR_2.2.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) mzR_2.2.2.tgz
Mac OS X 10.9 (Mavericks) mzR_2.2.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/mzR/tree/release-3.1
Package Short Url http://bioconductor.org/packages/mzR/
Package Downloads Report Download Stats

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