mzR

DOI: 10.18129/B9.bioc.mzR    

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

Bioconductor version: Release (3.14)

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, Johannes Rainer

Maintainer: Steffen Neumann <sneumann at ipb-halle.de>, Laurent Gatto <laurent.gatto at uclouvain.be>, Qiakng Kou <qkou at umail.iu.edu>

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("mzR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("mzR")

 

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

Details

biocViews	DataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version	2.28.0
In Bioconductor since	BioC 2.9 (R-2.14) (10.5 years)
License	Artistic-2.0
Depends	Rcpp (>= 0.10.1), methods, utils
Imports	Biobase, BiocGenerics(>= 0.13.6), ProtGenerics(>= 1.17.3), ncdf4
LinkingTo	Rcpp, zlibbioc, Rhdf5lib(>= 1.1.4)
Suggests	msdata(>= 0.15.1), RUnit, mzID, BiocStyle(>= 2.5.19), knitr, XML, rmarkdown
SystemRequirements	C++11, GNU make
Enhances
URL	https://github.com/sneumann/mzR/
BugReports	https://github.com/sneumann/mzR/issues/
Depends On Me	MSGFgui, MSnbase, proteomics
Imports Me	adductomicsR, Autotuner, CluMSID, DIAlignR, MSnID, msPurity, peakPantheR, ProteomicsAnnotationHubData, RMassBank, SIMAT, TargetDecoy, topdownr, xcms, yamss
Suggests Me	AnnotationHub, MsBackendRawFileReader, msdata, qcmetrics, RforProteomics, Spectra
Links To Me
Build Report

Package Archives

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

Source Package	mzR_2.28.0.tar.gz
Windows Binary	mzR_2.28.0.zip
macOS 10.13 (High Sierra)	mzR_2.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mzR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mzR
Package Short Url	https://bioconductor.org/packages/mzR/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive