MSnbase

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see MSnbase.

Base Functions and Classes for Mass Spectrometry and Proteomics


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

Details

biocViews DataImport, ImmunoOncology, Infrastructure, MassSpectrometry, Proteomics, QualityControl, Software
Version 2.8.3
In Bioconductor since BioC 2.8 (R-2.13) (13 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
System Requirements
URL https://github.com/lgatto/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(>= 1.7.1), msdata(>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle(>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny, magrittr, SummarizedExperiment
Linking To Rcpp
Enhances
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 Build Report

Package Archives

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

Source Package MSnbase_2.8.3.tar.gz
Windows Binary MSnbase_2.8.3.zip
Mac OS X 10.11 (El Capitan) MSnbase_2.8.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/MSnbase
Source Repository (Developer Access) git clone [email protected]:packages/MSnbase
Bioc Package Browser https://code.bioconductor.org/browse/MSnbase/
Package Short Url https://bioconductor.org/packages/MSnbase/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive