MSnbase

DOI: 10.18129/B9.bioc.MSnbase    

Base Functions and Classes for Mass Spectrometry and Proteomics

Bioconductor version: Release (3.8)

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 <lg390 at cam.ac.uk>

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("MSnbase", version = "3.8")

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 IO capabilities
HTML R Script MSnbase2 benchmarking
HTML R Script MSnbase: centroiding of profile-mode MS data
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software
Version 2.8.2
In Bioconductor since BioC 2.8 (R-2.13) (7.5 years)
License Artistic-2.0
Depends R (>= 3.1), methods, BiocGenerics(>= 0.7.1), Biobase(>= 2.15.2), mzR(>= 2.15.1), S4Vectors, ProtGenerics(>= 1.9.1)
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://github.com/lgatto/MSnbase
BugReports https://github.com/lgatto/MSnbase/issues
Depends On Me msmsEDA, msmsTests, ProCoNA, pRoloc, pRolocdata, pRolocGUI, proteomics, proteoQC, qPLEXanalyzer, RforProteomics, synapter, xcms
Imports Me DAPAR, DAPARdata, DEP, MSnID, MSstatsQC, Pbase, ProteomicsAnnotationHubData, qPLEXdata, RMassBank, topdownr
Suggests Me AnnotationHub, biobroom, BiocGenerics, isobar, msdata, qcmetrics, readat, rpx
Links To Me
Build Report  

Package Archives

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

Source Package MSnbase_2.8.2.tar.gz
Windows Binary MSnbase_2.8.2.zip
Mac OS X 10.11 (El Capitan) MSnbase_2.8.2.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 http://bioconductor.org/packages/MSnbase/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive

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