mzR

This package is for version 3.11 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: 3.11

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 "4.0") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version	2.22.0
In Bioconductor since	BioC 2.9 (R-2.14) (12.5 years)
License	Artistic-2.0
Depends	Rcpp (>= 0.10.1), methods, utils
Imports	Biobase, BiocGenerics(>= 0.13.6), ProtGenerics(>= 1.17.3), ncdf4
System Requirements	C++11, GNU make
URL	https://github.com/sneumann/mzR/
Bug Reports	https://github.com/sneumann/mzR/issues/

Suggests	msdata(>= 0.15.1), RUnit, mzID, BiocStyle(>= 2.5.19), knitr, XML
Linking To	Rcpp, zlibbioc, Rhdf5lib(>= 1.1.4)
Enhances
Depends On Me	MSGFgui, MSnbase, proteomics
Imports Me	adductomicsR, Autotuner, CluMSID, DIAlignR, MSnID, msPurity, peakPantheR, ProteomicsAnnotationHubData, RMassBank, SIMAT, topdownr, xcms, yamss
Suggests Me	AnnotationHub, msdata, qcmetrics, RforProteomics
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	mzR_2.22.0.tar.gz
Windows Binary	mzR_2.22.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	mzR_2.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mzR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mzR
Bioc Package Browser	https://code.bioconductor.org/browse/mzR/
Package Short Url	https://bioconductor.org/packages/mzR/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive