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DOI: 10.18129/B9.bioc.MSnbase    

Base Functions and Classes for Mass Spectrometry and Proteomics

Bioconductor version: Release (3.5)

Manipulation, processing and visualisation of mass spectrometry and 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
HTML R Script A short introduction to `MSnbase` development
HTML R Script MSnbase IO capabilities
HTML R Script MSnbase2 benchmarking
PDF   Reference Manual
Text   NEWS


biocViews DataImport, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software
Version 2.2.0
In Bioconductor since BioC 2.8 (R-2.13) (6.5 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, stats4, affy, impute, pcaMethods, mzID(>= 1.5.2), MALDIquant (>= 1.16), digest, lattice, ggplot2, S4Vectors, XML, Rcpp
LinkingTo Rcpp
Suggests testthat, pryr, reshape2, 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, xcms
Imports Me DAPAR, DAPARdata, MSnID, MSstats, Pbase, ProteomicsAnnotationHubData, RMassBank
Suggests Me AnnotationHub, biobroom, BiocGenerics, isobar, qcmetrics, readat, rpx
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