mzR

This is the released version of mzR; for the devel version, see mzR.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9

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

Bioconductor version: Release (3.23)

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")):

Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer. mzR: parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data). doi:10.18129/B9.bioc.mzR, R package version 2.46.0, https://bioconductor.org/packages/mzR.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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	2.46.0
In Bioconductor since	BioC 2.9 (R-2.14) (15 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/

Suggests	MsDataHub, RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML, rmarkdown
Linking To	Rcpp, Rhdf5lib (>= 1.1.4)
Enhances
Depends On Me	MSnbase
Imports Me	Aerith, CluMSID, lcmsPlot, MSnID, msPurity, peakPantheR, RMassBank, sfi, SIMAT, TargetDecoy, topdownr, xcms, yamss
Suggests Me	AnnotationHub, Chromatograms, chromConverter, erah, MetaboAnnotation, MsBackendMetaboLights, MsBackendRawFileReader, MsBackendSql, msdata, MsDataHub, MsExperiment, MsQuality, PSMatch, qcmetrics, RforProteomics, Spectra, SpectraQL, SpectriPy
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	mzR_2.46.0.tar.gz
Windows Binary (x86_64)	mzR_2.46.0.zip
macOS Binary (big-sur-x86_64)	mzR_2.46.0.tgz
macOS Binary (sonoma-arm64)	mzR_2.46.0.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