MetaboAnnotation

Utilities for Annotation of Metabolomics Data

Bioconductor version: Release (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

Details

biocViews	Infrastructure, MassSpectrometry, Metabolomics, Software
Version	1.4.1
In Bioconductor since	BioC 3.15 (R-4.2) (1.5 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, CompoundDb
Linking To
Suggests	testthat, knitr, msdata, BiocStyle, rmarkdown, plotly, shiny, shinyjs, DT, AnnotationHub, microbenchmark, mzR
System Requirements
Enhances	RMariaDB, RSQLite
URL	https://github.com/RforMassSpectrometry/MetaboAnnotation
Bug Reports	https://github.com/RforMassSpectrometry/MetaboAnnotation/issues

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	MetaboAnnotation_1.4.1.tar.gz
Windows Binary	MetaboAnnotation_1.4.1.zip (64-bit only)
macOS Binary (x86_64)	MetaboAnnotation_1.4.1.tgz
macOS Binary (arm64)	MetaboAnnotation_1.4.1.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 3.17	Source Archive