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

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 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
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

Details

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
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, xcms
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.

Source Package	MSnbase_2.2.0.tar.gz
Windows Binary	MSnbase_2.2.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	MSnbase_2.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MSnbase
Package Short Url	http://bioconductor.org/packages/MSnbase/
Package Downloads Report	Download Stats

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