MSnbase

DOI: 10.18129/B9.bioc.MSnbase    

Base Functions and Classes for Mass Spectrometry and Proteomics

Bioconductor version: Release (3.11)

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 and Lieven Clement.

Maintainer: Laurent Gatto <laurent.gatto at uclouvain.be>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	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
PDF		Reference Manual

Details

biocViews	DataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software
Version	2.14.2
In Bioconductor since	BioC 2.8 (R-2.13) (9.5 years)
License	Artistic-2.0
Depends	R (>= 3.5), methods, BiocGenerics(>= 0.7.1), Biobase(>= 2.15.2), mzR(>= 2.19.6), S4Vectors, ProtGenerics(>= 1.19.3)
Imports	BiocParallel, IRanges(>= 2.13.28), plyr, preprocessCore, 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	Autotuner, MetCirc, msmsEDA, msmsTests, pRoloc, pRolocdata, pRolocGUI, proteomics, proteoQC, qPLEXanalyzer, RforProteomics, synapter, xcms, xcms
Imports Me	cliqueMS, CluMSID, DAPAR, DAPARdata, DEP, MSnID, MSstatsQC, peakPantheR, PrInCE, ProteomicsAnnotationHubData, qPLEXdata, RMassBank, topdownr
Suggests Me	AnnotationHub, biobroom, BiocGenerics, isobar, msdata, proDA, qcmetrics, readat, rpx
Links To Me
Build Report

Package Archives

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

Source Package	MSnbase_2.14.2.tar.gz
Windows Binary	MSnbase_2.14.2.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	MSnbase_2.14.2.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 3.11	Source Archive