mzR
This package is for version 3.14 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: 3.14
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 <laurent.gatto at uclouvain.be>, Qiakng Kou <qkou at umail.iu.edu>
citation("mzR")):
Installation
To install this package, start R (version "4.1") 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 | ||
| NEWS | Text |
Details
| biocViews | DataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software |
| Version | 2.28.0 |
| 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/ |
See More
| Suggests | msdata(>= 0.15.1), RUnit, mzID, BiocStyle(>= 2.5.19), knitr, XML, rmarkdown |
| 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, TargetDecoy, topdownr, xcms, yamss |
| Suggests Me | AnnotationHub, MsBackendRawFileReader, msdata, 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_2.28.0.tar.gz |
| Windows Binary | mzR_2.28.0.zip |
| macOS 10.13 (High Sierra) | mzR_2.28.0.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 3.14 | Source Archive |