MetaboAnnotation

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see MetaboAnnotation.

Utilities for Annotation of Metabolomics Data

Bioconductor version: 3.17

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] , 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Infrastructure, MassSpectrometry, Metabolomics, Software
Version	1.4.3
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(>= 1.9.12), BiocParallel, SummarizedExperiment, QFeatures, graphics, AnnotationHub, CompoundDb
System Requirements
URL	https://github.com/RforMassSpectrometry/MetaboAnnotation
Bug Reports	https://github.com/RforMassSpectrometry/MetaboAnnotation/issues

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_1.4.3.tar.gz
Windows Binary	MetaboAnnotation_1.4.3.zip (64-bit only)
macOS Binary (x86_64)	MetaboAnnotation_1.4.3.tgz
macOS Binary (arm64)	MetaboAnnotation_1.4.3.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 3.17	Source Archive