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MetaboAnnotation

Utilities for Annotation of Metabolomics Data


Bioconductor version: Release (3.18)

High level functions to assist in annotation of (metabolomics) data sets. These include functions to perform simple tentative annotations based on mass matching but also functions to consider m/z and retention times for annotation of LC-MS features given that respective reference values are available. In addition, the function provides high-level functions to simplify matching of LC-MS/MS spectra against spectral libraries and objects and functionality to represent and manage such matched data.

Author: Michael Witting [aut] , Johannes Rainer [aut, cre] , Andrea Vicini [aut] , Carolin Huber [aut] , Philippine Louail [aut] , Nir Shachaf [ctb]

Maintainer: Johannes Rainer <Johannes.Rainer at eurac.edu>

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

Installation

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


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

BiocManager::install("MetaboAnnotation")

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("MetaboAnnotation")
Annotation of MS-based Metabolomics Data HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Infrastructure, MassSpectrometry, Metabolomics, Software
Version 1.6.1
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License Artistic-2.0
Depends R (>= 4.0.0)
Imports BiocGenerics, MsCoreUtils, MetaboCoreUtils, ProtGenerics, methods, S4Vectors, Spectra(>= 1.11.10), BiocParallel, SummarizedExperiment, QFeatures, AnnotationHub, graphics, CompoundDb
System Requirements
URL https://github.com/RforMassSpectrometry/MetaboAnnotation
Bug Reports https://github.com/RforMassSpectrometry/MetaboAnnotation/issues
See More
Suggests testthat, knitr, msdata, BiocStyle, rmarkdown, plotly, shiny, shinyjs, DT, microbenchmark, mzR
Linking To
Enhances RMariaDB, RSQLite
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package MetaboAnnotation_1.6.1.tar.gz
Windows Binary MetaboAnnotation_1.6.1.zip
macOS Binary (x86_64) MetaboAnnotation_1.6.1.tgz
macOS Binary (arm64) MetaboAnnotation_1.6.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/MetaboAnnotation
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MetaboAnnotation
Bioc Package Browser https://code.bioconductor.org/browse/MetaboAnnotation/
Package Short Url https://bioconductor.org/packages/MetaboAnnotation/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive