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mzR

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


Bioconductor version: Release (3.18)

mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a subset of the proteowizard library for mzXML, 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>

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

Installation

To install this package, start R (version "4.3") 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

Details

biocViews DataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version 2.36.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License Artistic-2.0
Depends R (>= 4.0.0), 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/
See More
Suggests msdata(>= 0.15.1), RUnit, mzID, BiocStyle(>= 2.5.19), knitr, XML, rmarkdown
Linking To Rcpp, Rhdf5lib(>= 1.1.4)
Enhances
Depends On Me MSnbase
Imports Me adductomicsR, CluMSID, DIAlignR, MSnID, msPurity, peakPantheR, RMassBank, SIMAT, TargetDecoy, topdownr, xcms, yamss
Suggests Me AnnotationHub, MetaboAnnotation, MsBackendRawFileReader, MsBackendSql, msdata, MsDataHub, MsExperiment, MsQuality, PSMatch, qcmetrics, RforProteomics, Spectra
Links To Me
Build Report Build Report

Package Archives

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

Source Package mzR_2.36.0.tar.gz
Windows Binary mzR_2.36.0.zip
macOS Binary (x86_64) mzR_2.36.0.tgz
macOS Binary (arm64) mzR_2.36.0.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