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MsExperiment

Infrastructure for Mass Spectrometry Experiments


Bioconductor version: Release (3.18)

Infrastructure to store and manage all aspects related to a complete proteomics or metabolomics mass spectrometry (MS) experiment. The MsExperiment package provides light-weight and flexible containers for MS experiments building on the new MS infrastructure provided by the Spectra, QFeatures and related packages. Along with raw data representations, links to original data files and sample annotations, additional metadata or annotations can also be stored within the MsExperiment container. To guarantee maximum flexibility only minimal constraints are put on the type and content of the data within the containers.

Author: Laurent Gatto [aut, cre] , Johannes Rainer [aut] , Sebastian Gibb [aut]

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

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

Installation

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


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

BiocManager::install("MsExperiment")

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("MsExperiment")
Managing Mass Spectrometry Experiments HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, ExperimentalDesign, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version 1.4.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License Artistic-2.0
Depends R (>= 4.2), ProtGenerics(>= 1.9.1)
Imports methods, S4Vectors, IRanges, Spectra, SummarizedExperiment, QFeatures
System Requirements
URL https://github.com/RforMassSpectrometry/MsExperiment
Bug Reports https://github.com/RforMassSpectrometry/MsExperiment/issues
See More
Suggests testthat, knitr (>= 1.1.0), roxygen2, BiocStyle(>= 2.5.19), rmarkdown, rpx, mzR, msdata
Linking To
Enhances
Depends On Me
Imports Me MsQuality, xcms
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package MsExperiment_1.4.0.tar.gz
Windows Binary MsExperiment_1.4.0.zip (64-bit only)
macOS Binary (x86_64) MsExperiment_1.4.0.tgz
macOS Binary (arm64) MsExperiment_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MsExperiment
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MsExperiment
Bioc Package Browser https://code.bioconductor.org/browse/MsExperiment/
Package Short Url https://bioconductor.org/packages/MsExperiment/
Package Downloads Report Download Stats