MSnbase

This is the released version of MSnbase; for the devel version, see MSnbase.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8

Base Functions and Classes for Mass Spectrometry and Proteomics

Bioconductor version: Release (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 (from within R, enter citation("MSnbase")):

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. MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics. doi:10.18129/B9.bioc.MSnbase, R package version 2.38.1, https://bioconductor.org/packages/MSnbase.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

BiocManager::install("MSnbase")

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("MSnbase")

Base Functions and Classes for MS-based Proteomics	HTML	R Script
MSnbase IO capabilities	HTML	R Script
MSnbase: centroiding of profile-mode MS data	HTML	R Script
MSnbase benchmarking	HTML	R Script
A short introduction to `MSnbase` development	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software
Version	2.38.1
In Bioconductor since	BioC 2.8 (R-2.13) (15.5 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 (>= 1.15.3), PTMods (>= 0.99.5), 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

Suggests	testthat, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), Rdisop, pRoloc, pRolocdata (>= 1.43.3), magick, MsDataHub, msdata, 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, DAPARdata, MetaboAnnotatoR, msmsEDA, msmsTests, pRoloc, pRolocdata, pRolocGUI, qPLEXanalyzer, RforProteomics
Imports Me	Aerith, cliqueMS, CluMSID, DAPAR, lcmsPlot, MSnID, MSstatsQC, omXplore, peakPantheR, PrInCE, PRONE, ptairMS, qPLEXanalyzer, qPLEXdata, RMassBank, squallms, topdownr, xcms
Suggests Me	AnnotationHub, biobroom, BiocGenerics, faahKO, isobar, LCMSQA, msdata, msPurity, msqrob2, mtbls2, PepMapViz, proDA, qcmetrics, qPLEXanalyzer, wpm
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	MSnbase_2.38.1.tar.gz
Windows Binary (x86_64)	MSnbase_2.38.1.zip
macOS Binary (big-sur-x86_64)	MSnbase_2.37.0.tgz
macOS Binary (sonoma-arm64)	MSnbase_2.38.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MSnbase
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MSnbase
Package Short Url	https://bioconductor.org/packages/MSnbase/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.23	Source Archive