mzR

DOI: 10.18129/B9.bioc.mzR    

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

Bioconductor version: Release (3.6)

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>

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

HTML	R Script	Accessin raw mass spectrometry and identification data
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version	2.12.0
In Bioconductor since	BioC 2.9 (R-2.14) (6.5 years)
License	Artistic-2.0
Depends	Rcpp (>= 0.10.1), methods, utils
Imports	Biobase, BiocGenerics(>= 0.13.6), ProtGenerics(>= 1.9.1)
LinkingTo	Rcpp, zlibbioc
Suggests	msdata(>= 0.15.1), RUnit, mzID, BiocStyle(>= 2.5.19), knitr, XML
SystemRequirements	C++11, GNU make, NetCDF
Enhances
URL	https://github.com/sneumann/mzR/
BugReports	https://github.com/sneumann/mzR/issues/
Depends On Me	MSGFgui, MSnbase
Imports Me	MSnID, msPurity, Pbase, ProteomicsAnnotationHubData, RMassBank, SIMAT, topdownr, xcms, yamss
Suggests Me	AnnotationHub, msdata, qcmetrics, RforProteomics
Build Report

Package Archives

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

Source Package	mzR_2.12.0.tar.gz
Windows Binary	mzR_2.12.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	mzR_2.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mzR
Package Short Url	http://bioconductor.org/packages/mzR/
Package Downloads Report	Download Stats