mzR
parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
DOI: 10.18129/B9.bioc.mzR
Bioconductor version: Release (3.20)
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("mzR")):
Installation
To install this package, start R (version "4.4") 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 | 2.40.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (13 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.
| Source Package | mzR_2.40.0.tar.gz |
| Windows Binary (x86_64) | mzR_2.40.0.zip |
| macOS Binary (x86_64) | mzR_2.40.0.tgz |
| macOS Binary (arm64) | mzR_2.40.0.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 |