DOI: 10.18129/B9.bioc.MSnbase    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see MSnbase.

Base Functions and Classes for Mass Spectrometry and Proteomics

Bioconductor version: 3.8

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 <lg390 at>

Citation (from within R, enter citation("MSnbase")):


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

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


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HTML R Script A short introduction to `MSnbase` development
HTML R Script Base Functions and Classes for MS-based Proteomics
HTML R Script MSnbase IO capabilities
HTML R Script MSnbase2 benchmarking
HTML R Script MSnbase: centroiding of profile-mode MS data
PDF   Reference Manual
Text   NEWS


biocViews DataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software
Version 2.8.3
In Bioconductor since BioC 2.8 (R-2.13) (8 years)
License Artistic-2.0
Depends R (>= 3.1), methods, BiocGenerics(>= 0.7.1), Biobase(>= 2.15.2), mzR(>= 2.15.1), S4Vectors, ProtGenerics(>= 1.9.1)
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
Depends On Me msmsEDA, msmsTests, ProCoNA, pRoloc, pRolocdata, pRolocGUI, proteomics, proteoQC, qPLEXanalyzer, RforProteomics, synapter, xcms
Imports Me DAPAR, DAPARdata, DEP, MSnID, MSstatsQC, Pbase, ProteomicsAnnotationHubData, qPLEXdata, RMassBank, topdownr
Suggests Me AnnotationHub, biobroom, BiocGenerics, isobar, msdata, qcmetrics, readat, rpx
Links To Me
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Source Package MSnbase_2.8.3.tar.gz
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Mac OS X 10.11 (El Capitan) MSnbase_2.8.3.tgz
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