MSnbase

DOI: 10.18129/B9.bioc.MSnbase    

Base Functions and Classes for Mass Spectrometry and Proteomics

Bioconductor version: Release (3.6)

MSnbase provides infrastructure to manipulation, processing and visualisation mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.

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

Maintainer: Laurent Gatto <lg390 at cam.ac.uk>

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

HTML	R Script	A short introduction to `MSnbase` development
HTML	R Script	Base Functions and Classes for MS-based Proteomics
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	2.4.2
In Bioconductor since	BioC 2.8 (R-2.13) (7 years)
License	Artistic-2.0
Depends	R (>= 3.1), methods, BiocGenerics(>= 0.7.1), Biobase(>= 2.15.2), mzR(>= 2.11.11), BiocParallel, ProtGenerics(>= 1.9.1)
Imports	plyr, IRanges, preprocessCore, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID(>= 1.5.2), 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(>= 2.5.19), 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, DEP, MSnID, MSstats, MSstatsQC, Pbase, ProteomicsAnnotationHubData, RMassBank, topdownr
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_2.4.2.tar.gz
Windows Binary	MSnbase_2.4.2.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	MSnbase_2.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MSnbase
Package Short Url	http://bioconductor.org/packages/MSnbase/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive