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MSnbase

Base Functions and Classes for Mass Spectrometry and Proteomics


Bioconductor version: Release (3.19)

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")):

Installation

To install this package, start R (version "4.4") 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")
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 PDF

Details

biocViews DataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software
Version 2.30.1
In Bioconductor since BioC 2.8 (R-2.13) (13 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, 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(>= 1.7.1), msdata(>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle(>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, XML, shiny, magrittr, SummarizedExperiment
Linking To Rcpp
Enhances
Depends On Me bandle, msmsEDA, msmsTests, pRoloc, pRolocGUI, qPLEXanalyzer, synapter, DAPARdata, pRolocdata, RforProteomics
Imports Me CluMSID, DAPAR, DEP, MSnID, MSstatsQC, peakPantheR, PrInCE, ptairMS, topdownr, xcms, qPLEXdata
Suggests Me AnnotationHub, biobroom, BiocGenerics, isobar, msPurity, msqrob2, proDA, qcmetrics, wpm, msdata, enviGCMS, LCMSQA, pmd, RAMClustR
Links To Me
Build Report Build Report

Package Archives

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

Source Package MSnbase_2.30.1.tar.gz
Windows Binary MSnbase_2.30.1.zip
macOS Binary (x86_64) MSnbase_2.30.1.tgz
macOS Binary (arm64) MSnbase_2.30.1.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