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mzR

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

Bioconductor version: 3.23 · Package version: 2.46.0

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.

Installation

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

BiocManager::install("mzR")

Details

MaintainerSteffen Neumann <sneumann@ipb-halle.de>
AuthorBernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer
LicenseArtistic-2.0
URLhttps://github.com/sneumann/mzR/
Bug Reportshttps://github.com/sneumann/mzR/issues/
System RequirementsC++11, GNU make
Downloads rank4739
Source branchRELEASE_3_23
biocViewsDataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software

Documentation

Download

Dependencies

Depends: R (>= 4.0.0), Rcpp (>= 0.10.1), methods, utils

Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3), ncdf4

LinkingTo: Rcpp, Rhdf5lib (>= 1.1.4)

Suggests: MsDataHub, RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML, rmarkdown

Reverse dependencies

Depends On Me (1): MSnbase

Imports Me (13): Aerith, CluMSID, lcmsPlot, MSnID, msPurity, peakPantheR, RMassBank, sfi, SIMAT, TargetDecoy, topdownr, xcms, yamss

Suggests Me (18): AnnotationHub, Chromatograms, chromConverter, erah, MetaboAnnotation, MsBackendMetaboLights, MsBackendRawFileReader, MsBackendSql, msdata, MsDataHub, MsExperiment, MsQuality, PSMatch, qcmetrics, RforProteomics, Spectra, SpectraQL, SpectriPy