MSnbase

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

Base Functions and Classes for Mass Spectrometry and Proteomics

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DOI: 10.18129/B9.bioc.MSnbase

Bioconductor version: Release (3.22)

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")

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 HTML R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software

Version 2.36.0

In Bioconductor since BioC 2.8 (R-2.13) (14.5 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(>= 1.13.2), 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

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, 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, mtbls2, LCMSQA, PepMapViz

Links To Me

Build Report Build Report

Package Archives

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

Source Package MSnbase_2.36.0.tar.gz

Windows Binary (x86_64) MSnbase_2.36.0.zip

macOS Binary (x86_64) MSnbase_2.36.0.tgz

macOS Binary (arm64) MSnbase_2.36.0.tgz

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/

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