To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MSnbase")

In most cases, you don't need to download the package archive at all.

MSnbase

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 cam.ac.uk> 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 cam.ac.uk>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MSnbase")

Documentation

To view documentation for the version of this package installed in your system, start R and enter: 

browseVignettes("MSnbase")
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

Details

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
SystemRequirements
Enhances
URL https://github.com/lgatto/MSnbase
BugReports https://github.com/lgatto/MSnbase/issues
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
Build Report

Package Archives

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

Package Source MSnbase_2.0.2.tar.gz
Windows Binary MSnbase_2.0.2.zip (32- & 64-bit)
Mac OS X 10.9 (Mavericks) MSnbase_2.0.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/MSnbase/tree/release-3.4
Package Short Url http://bioconductor.org/packages/MSnbase/
Package Downloads Report Download Stats

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