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This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see MSnbase.

Base Functions and Classes for MS-based Proteomics

Bioconductor version: 3.4

Basic plotting, data manipulation and processing of MS-based Proteomics data.

Author: Laurent Gatto <lg390 at> with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Martina Fisher, Johannes Rainer and Sebastian Gibb.

Maintainer: Laurent Gatto <lg390 at>

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


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PDF R Script Base Functions and Classes for MS-based Proteomics
PDF R Script MSnbase development
PDF R Script MSnbase IO capabilities
HTML R Script MSnbase benchmarking
PDF   Reference Manual
Text   NEWS


biocViews DataImport, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software
Version 2.0.2
In Bioconductor since BioC 2.8 (R-2.13) (6 years)
License Artistic-2.0
Depends R (>= 3.1), methods, BiocGenerics(>= 0.7.1), Biobase(>= 2.15.2), mzR(>= 2.7.6), BiocParallel, ProtGenerics(>= 1.5.1)
Imports plyr, IRanges, preprocessCore, vsn, grid, reshape2, stats4, affy, impute, pcaMethods, mzID(>= 1.5.2), MALDIquant (>= 1.12), digest, lattice, ggplot2, S4Vectors, XML, Rcpp
LinkingTo Rcpp
Suggests testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata(>= 1.7.1), msdata(>= 0.12.2), roxygen2, rgl, rpx, AnnotationHub, BiocStyle, rmarkdown, imputeLCMD, norm, gplots, shiny
Depends On Me msmsEDA, msmsTests, ProCoNA, pRoloc, pRolocdata, pRolocGUI, proteoQC, RforProteomics, synapter
Imports Me DAPAR, DAPARdata, MSnID, MSstats, Pbase, ProteomicsAnnotationHubData, RMassBank
Suggests Me AnnotationHub, biobroom, BiocGenerics, isobar, qcmetrics, readat, rpx
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