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Bioconductor - mzR (development version)

mzR

This is the development version of mzR; for the stable release version, see mzR.

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

Bioconductor version: Development (3.22)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 2.43.0 In Bioconductor since BioC 2.9 (R-2.14) (13.5 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, MSnID, msPurity, peakPantheR, RMassBank, SIMAT, TargetDecoy, topdownr, xcms, yamss Suggests Me AnnotationHub, koinar, MetaboAnnotation, MsBackendMetaboLights, MsBackendRawFileReader, MsBackendSql, MsDataHub, MsExperiment, MsQuality, PSMatch, qcmetrics, Spectra, SpectraQL, msdata, RforProteomics, chromConverter, erah Links To Me Build Report Build Report Package Archives

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

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