MSnbase

DOI: 10.18129/B9.bioc.MSnbase  

This is the development version of MSnbase; for the stable release version, see MSnbase.

Base Functions and Classes for Mass Spectrometry and Proteomics

Bioconductor version: Development (3.18)

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, Lieven Clement and Pascal Maas.

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

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

Installation

To install this package, start R (version "4.3") and enter:

if (!require("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

PDF   Reference Manual

Details

biocViews DataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software
Version 2.27.0
In Bioconductor since BioC 2.8 (R-2.13) (12 years)
License Artistic-2.0
Depends R (>= 3.5), methods, BiocGenerics(>= 0.7.1), Biobase(>= 2.15.2), mzR(>= 2.29.3), S4Vectors, ProtGenerics(>= 1.29.1)
Imports MsCoreUtils, BiocParallel, IRanges(>= 2.13.28), plyr, 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 bandle, DAPARdata, MobilityTransformR, msmsEDA, msmsTests, pRoloc, pRolocdata, pRolocGUI, qPLEXanalyzer, RforProteomics, synapter, xcms
Imports Me cliqueMS, CluMSID, DAPAR, DEP, MSnID, MSstatsQC, peakPantheR, PrInCE, ptairMS, qPLEXdata, RMassBank, topdownr
Suggests Me AnnotationHub, biobroom, BiocGenerics, isobar, msdata, msPurity, msqrob2, proDA, qcmetrics, wpm
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary MSnbase_2.27.0.zip (64-bit only)
macOS Binary (x86_64) MSnbase_2.27.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/MSnbase
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MSnbase
Bioc Package Browser https://code.bioconductor.org/browse/MSnbase/
Package Short Url https://bioconductor.org/packages/MSnbase/
Package Downloads Report Download Stats

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