MetCirc

DOI: 10.18129/B9.bioc.MetCirc    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see MetCirc.

Navigating mass spectral similarity in high-resolution MS/MS metabolomics data

Bioconductor version: 3.12

MetCirc comprises a workflow to interactively explore high-resolution MS/MS metabolomics data. MetCirc uses the Spectrum2 and MSpectra infrastructure defined in the package MSnbase that stores MS/MS spectra. MetCirc offers functionality to calculate similarity between precursors based on the normalised dot product, neutral losses or user-defined functions and visualise similarities in a circular layout. Within the interactive framework the user can annotate MS/MS features based on their similarity to (known) related MS/MS features.

Author: Thomas Naake <thomasnaake at googlemail.com>, Johannes Rainer <johannes.rainer at eurac.edu> and Emmanuel Gaquerel <emmanuel.gaquerel at ibmp-cnrs.unistra.fr>

Maintainer: Thomas Naake <thomasnaake at googlemail.com>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("MetCirc")

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("MetCirc")

 

PDF	R Script	Workflow for Metabolomics
PDF		Reference Manual
Text		NEWS

Details

biocViews	ImmunoOncology, MassSpectrometry, Metabolomics, Software, Visualization
Version	1.20.0
In Bioconductor since	BioC 3.4 (R-3.3) (4.5 years)
License	GPL (>= 3)
Depends	R (>= 3.5), amap (>= 0.8), circlize (>= 0.3.9), scales (>= 0.3.0), shiny (>= 1.0.0), MSnbase(>= 2.15.3)
Imports	ggplot2 (>= 3.2.1), S4Vectors(>= 0.22.0)
LinkingTo
Suggests	BiocGenerics, graphics (>= 3.5), grDevices (>= 3.5), knitr (>= 1.11), methods (>= 3.5), stats (>= 3.5), testthat (>= 2.2.1)
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Build Report

Package Archives

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

Source Package	MetCirc_1.20.0.tar.gz
Windows Binary	MetCirc_1.20.0.zip
macOS 10.13 (High Sierra)	MetCirc_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MetCirc
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MetCirc
Package Short Url	https://bioconductor.org/packages/MetCirc/
Package Downloads Report	Download Stats