MsExperiment

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16

Infrastructure for Mass Spectrometry Experiments

Bioconductor version: Development (3.24)

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] ORCID: 0000-0002-1520-2268 , Johannes Rainer [aut] ORCID: 0000-0002-6977-7147 , Sebastian Gibb [aut] ORCID: 0000-0001-7406-4443 , Tuomas Borman [ctb] ORCID: 0000-0002-8563-8884

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

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

Laurent Gatto, Johannes Rainer, Sebastian Gibb. MsExperiment: Infrastructure for Mass Spectrometry Experiments. doi:10.18129/B9.bioc.MsExperiment, R package version 1.15.0, https://bioconductor.org/packages/MsExperiment.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, ExperimentalDesign, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software
Version	1.15.0
In Bioconductor since	BioC 3.16 (R-4.2) (4 years)
License	Artistic-2.0
Depends	R (>= 4.2), ProtGenerics (>= 1.35.2)
Imports	methods, S4Vectors, IRanges, Spectra, SummarizedExperiment, QFeatures, DBI, BiocGenerics
System Requirements
URL	https://github.com/RforMassSpectrometry/MsExperiment
Bug Reports	https://github.com/RforMassSpectrometry/MsExperiment/issues

Suggests	testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19), rmarkdown, rpx, mzR, MsDataHub, MsBackendSql (>= 1.3.2), RSQLite
Linking To
Enhances
Depends On Me
Imports Me	lcmsPlot, MsQuality, squallms, xcms
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	MsExperiment_1.15.0.tar.gz
Windows Binary (x86_64)	MsExperiment_1.15.0.zip
macOS Binary (big-sur-x86_64)	MsExperiment_1.15.0.tgz
macOS Binary (sonoma-arm64)	MsExperiment_1.15.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MsExperiment
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MsExperiment
Package Short Url	https://bioconductor.org/packages/MsExperiment/
Package Downloads Report	Download Stats