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MSnbase
This is thedevelopment version of MSnbase; for the stable release version, seeMSnbase.
Base Functions and Classes for Mass Spectrometry and Proteomics
Bioconductor version: Development (3.23)
MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.
Author: Laurent Gatto, Johannes Rainer and Sebastian Gibb with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker, Lieven Clement and Pascal Maas.
Maintainer: Laurent Gatto <laurent.gatto at uclouvain.be>
citation("MSnbase")):Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")# The following initializes usage of Bioc develBiocManager::install(version='devel')BiocManager::install("MSnbase")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("MSnbase")| A short introduction to `MSnbase` development | HTML | R Script |
| Base Functions and Classes for MS-based Proteomics | HTML | R Script |
| MSnbase benchmarking | HTML | R Script |
| MSnbase IO capabilities | HTML | R Script |
| MSnbase: centroiding of profile-mode MS data | HTML | R Script |
| Reference Manual |
Details
| biocViews | DataImport,ImmunoOncology,Infrastructure,MassSpectrometry,Proteomics,QualityControl,Software |
| Version | 2.37.0 |
| In Bioconductor since | BioC 2.8 (R-2.13) (14.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5), methods,BiocGenerics(>= 0.7.1),Biobase(>= 2.15.2),mzR(>= 2.29.3),S4Vectors,ProtGenerics(>= 1.29.1) |
| Imports | MsCoreUtils,PSMatch(>= 1.13.2),BiocParallel,IRanges(>= 2.13.28),plyr,vsn, grid, stats4,affy,impute,pcaMethods,MALDIquant (>= 1.16),mzID(>= 1.5.2),digest,lattice,ggplot2,scales,MASS,Rcpp |
| System Requirements | |
| URL | https://lgatto.github.io/MSnbase |
| Bug Reports | https://github.com/lgatto/MSnbase/issues |
See More
| Suggests | testthat,pryr,gridExtra,microbenchmark,zoo,knitr (>= 1.1.0),rols,Rdisop,pRoloc,pRolocdata(>= 1.43.3),magick,msdata(>= 0.19.3),roxygen2,rgl,rpx,AnnotationHub,BiocStyle(>= 2.5.19),rmarkdown,imputeLCMD,norm,gplots,XML,shiny,magrittr,SummarizedExperiment,Spectra |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | bandle,msmsEDA,msmsTests,pRoloc,pRolocGUI,DAPARdata,pRolocdata,RforProteomics |
| Imports Me | Aerith,cliqueMS,CluMSID,DAPAR,MSnID,MSstatsQC,peakPantheR,PrInCE,PRONE,ptairMS,RMassBank,squallms,topdownr,xcms |
| Suggests Me | AnnotationHub,biobroom,BiocGenerics,isobar,msPurity,msqrob2,qcmetrics,wpm,faahKO,msdata,mtbls2,LCMSQA,PepMapViz |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | MSnbase_2.37.0.tar.gz |
| Windows Binary (x86_64) | MSnbase_2.37.0.zip |
| macOS Binary (x86_64) | MSnbase_2.37.0.tgz |
| macOS Binary (arm64) | MSnbase_2.37.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MSnbase |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MSnbase |
| Bioc Package Browser | https://code.bioconductor.org/browse/MSnbase/ |
| Package Short Url | https://bioconductor.org/packages/MSnbase/ |
| Package Downloads Report | Download Stats |