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

Base Functions and Classes for MS-based Proteomics

Bioconductor version: Development (3.5)

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 2.1.0
In Bioconductor since BioC 2.8 (R-2.13) (5.5 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, pRolocGUI, proteoQC, synapter
Imports Me DAPAR, MSnID, MSstats, Pbase, ProteomicsAnnotationHubData, RMassBank
Suggests Me AnnotationHub, biobroom, BiocGenerics, isobar, qcmetrics, readat, rpx
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