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Bioconductor - MSnbase

MSnbase

This is the released version of MSnbase; for the devel version, see MSnbase.

Base Functions and Classes for Mass Spectrometry and Proteomics

Bioconductor version: Release (3.21)

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 "4.5") and enter:


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

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")

Details biocViews DataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software Version 2.34.1 In Bioconductor since BioC 2.8 (R-2.13) (14 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, PSMatch, BiocParallel, IRanges(>= 2.13.28), plyr, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16), mzID(>= 1.5.2), digest, lattice, ggplot2, scales, MASS, Rcpp System Requirements URL https://lgatto.github.io/MSnbase Bug Reports https://github.com/lgatto/MSnbase/issues See More Suggests testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata(>= 1.43.3), magick, msdata(>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle(>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, XML, shiny, magrittr, SummarizedExperiment, Spectra Linking To Rcpp Enhances Depends On Me bandle, msmsEDA, msmsTests, pRoloc, pRolocGUI, qPLEXanalyzer, synapter, DAPARdata, pRolocdata, RforProteomics Imports Me cliqueMS, CluMSID, DAPAR, DEP, MSnID, MSstatsQC, omXplore, peakPantheR, PrInCE, PRONE, ptairMS, RMassBank, squallms, topdownr, xcms, qPLEXdata Suggests Me AnnotationHub, biobroom, BiocGenerics, isobar, msPurity, msqrob2, proDA, qcmetrics, wpm, faahKO, msdata, LCMSQA, PepMapViz Links To Me Build Report Build Report Package Archives

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

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