mzR

DOI: 10.18129/B9.bioc.mzR    

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

Bioconductor version: Release (3.8)

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 <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 (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("mzR", version = "3.8")

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, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version 2.16.0
In Bioconductor since BioC 2.9 (R-2.14) (7 years)
License Artistic-2.0
Depends Rcpp (>= 0.10.1), methods, utils
Imports Biobase, BiocGenerics(>= 0.13.6), ProtGenerics(>= 1.9.1), ncdf4
LinkingTo Rcpp, zlibbioc, Rhdf5lib(>= 1.1.4)
Suggests msdata(>= 0.15.1), RUnit, mzID, BiocStyle(>= 2.5.19), knitr, XML
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 MSnID, msPurity, Pbase, ProteomicsAnnotationHubData, RMassBank, SIMAT, topdownr, xcms, yamss
Suggests Me AnnotationHub, msdata, qcmetrics, RforProteomics
Links To Me
Build Report  

Package Archives

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

Source Package mzR_2.16.0.tar.gz
Windows Binary mzR_2.16.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) mzR_2.16.0.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 http://bioconductor.org/packages/mzR/
Package Downloads Report Download Stats

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