mzR
This is thereleased version of mzR; for the devel version, seemzR.
parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
DOI: 10.18129/B9.bioc.mzR
Bioconductor version: Release (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("mzR")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("mzR")For older versions of R, please refer to the appropriateBioconductor 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 | 2.44.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (14 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,Chromatograms,koinar,MetaboAnnotation,MsBackendMetaboLights,MsBackendRawFileReader,MsBackendSql,MsDataHub,MsExperiment,MsQuality,PSMatch,qcmetrics,Spectra,SpectraQL,SpectriPy,msdata,RforProteomics,chromConverter,erah |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | mzR_2.44.0.tar.gz |
| Windows Binary (x86_64) | mzR_2.44.0.zip |
| macOS Binary (x86_64) | mzR_2.44.0.tgz |
| macOS Binary (arm64) | mzR_2.44.0.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 |