MSnbase

DOI: 10.18129/B9.bioc.MSnbase  

This is the development version of MSnbase; for the stable release version, see MSnbase.

Base Functions and Classes for Mass Spectrometry and Proteomics

Bioconductor version: Development (3.18)

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>

Installation

To install this package, start R (version "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MSnbase")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	DataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software
Version	2.27.0
In Bioconductor since	BioC 2.8 (R-2.13) (12 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, BiocParallel, IRanges(>= 2.13.28), plyr, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID(>= 1.5.2), digest, lattice, ggplot2, XML, scales, MASS, Rcpp
LinkingTo	Rcpp
Suggests	testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata(>= 1.7.1), msdata(>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle(>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny, magrittr, SummarizedExperiment
SystemRequirements
Enhances
URL	https://lgatto.github.io/MSnbase
BugReports	https://github.com/lgatto/MSnbase/issues
Depends On Me	bandle, DAPARdata, MobilityTransformR, msmsEDA, msmsTests, pRoloc, pRolocdata, pRolocGUI, qPLEXanalyzer, RforProteomics, synapter, xcms
Imports Me	cliqueMS, CluMSID, DAPAR, DEP, MSnID, MSstatsQC, peakPantheR, PrInCE, ptairMS, qPLEXdata, RMassBank, topdownr
Suggests Me	AnnotationHub, biobroom, BiocGenerics, isobar, msdata, msPurity, msqrob2, proDA, qcmetrics, wpm
Links To Me
Build Report

Package Archives

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

Source Package
Windows Binary	MSnbase_2.27.0.zip (64-bit only)
macOS Binary (x86_64)	MSnbase_2.27.0.tgz
macOS Binary (arm64)
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