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>

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

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

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