MSnbase

DOI: 10.18129/B9.bioc.MSnbase    

This is the development version of MSnbase; to use it, please install the devel version of Bioconductor.

Base Functions and Classes for Mass Spectrometry and Proteomics

Bioconductor version: Development (3.10)

MSnbase provides infrastructure for manipulation, processing and visualisation of 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, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker and Lieven Clement.

Maintainer: Laurent Gatto <laurent.gatto at uclouvain.be>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MSnbase")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("MSnbase")

 

HTML R Script A short introduction to `MSnbase` development
HTML R Script Base Functions and Classes for MS-based Proteomics
HTML R Script MSnbase benchmarking
HTML R Script MSnbase IO capabilities
HTML R Script MSnbase: centroiding of profile-mode MS data
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software
Version 2.11.10
In Bioconductor since BioC 2.8 (R-2.13) (8.5 years)
License Artistic-2.0
Depends R (>= 3.5.0), methods, BiocGenerics(>= 0.7.1), Biobase(>= 2.15.2), mzR(>= 2.19.6), S4Vectors, ProtGenerics(>= 1.17.4)
Imports BiocParallel, IRanges(>= 2.13.28), plyr, preprocessCore, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID(>= 1.5.2), digest, lattice, ggplot2, XML, scales, MASS, Rcpp
LinkingTo Rcpp
Suggests testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata(>= 1.7.1), msdata(>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle(>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny, magrittr, SummarizedExperiment
SystemRequirements
Enhances
URL https://lgatto.github.io/MSnbase
BugReports https://github.com/lgatto/MSnbase/issues
Depends On Me MetCirc, msmsEDA, msmsTests, pRoloc, pRolocdata, pRolocGUI, proteomics, proteoQC, qPLEXanalyzer, RforProteomics, synapter, xcms
Imports Me Autotuner, CluMSID, DAPAR, DAPARdata, DEP, MSnID, MSstatsQC, Pbase, peakPantheR, PrInCE, ProteomicsAnnotationHubData, qPLEXdata, RMassBank, topdownr
Suggests Me AnnotationHub, biobroom, BiocGenerics, isobar, msdata, proDA, qcmetrics, readat, rpx
Links To Me
Build Report  

Package Archives

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

Source Package MSnbase_2.11.10.tar.gz
Windows Binary MSnbase_2.11.10.zip
Mac OS X 10.11 (El Capitan) MSnbase_2.11.10.tgz
Source Repository git clone https://git.bioconductor.org/packages/MSnbase
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MSnbase
Package Short Url https://bioconductor.org/packages/MSnbase/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: