MetCirc

DOI: 10.18129/B9.bioc.MetCirc    

This is the development version of MetCirc; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (3.10)

MetCirc comprises a workflow to interactively explore high-resolution MS/MS metabolomics data. MetCirc uses the Spectrum2 and Spectra 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> and Emmanuel Gaquerel <emmanuel.gaquerel at ibmp-cnrs.unistra.fr>

Maintainer: Thomas Naake <thomasnaake at googlemail.com>

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

Installation

To install this package, start R (version "3.6") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.15.2
In Bioconductor since BioC 3.4 (R-3.3) (3 years)
License GPL (>= 3)
Depends R (>= 3.5), amap (>= 0.8), circlize (>= 0.3.9), scales (>= 0.3.0), shiny (>= 1.0.0), MSnbase(>= 2.10.1)
Imports ggplot2 (>= 3.2.1), S4Vectors(>= 0.22.0)
LinkingTo
Suggests BiocGenerics, graphics (>= 3.5), grDevices (>= 3.5), knitr (>= 1.11), methods (>= 3.5), RUnit (>= 0.4.32), stats (>= 3.5)
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Enhances
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Build Report  

Package Archives

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

Source Package MetCirc_1.15.2.tar.gz
Windows Binary MetCirc_1.15.2.zip
Mac OS X 10.11 (El Capitan) MetCirc_1.15.2.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

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