MetCirc

This package is for version 3.14 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: 3.14

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>

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

Installation

To install this package, start R (version "4.1") and enter:


if (!require("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")

Workflow for Metabolomics PDF R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ImmunoOncology, MassSpectrometry, Metabolomics, Software, Visualization

Version 1.24.0

In Bioconductor since BioC 3.4 (R-3.3) (7.5 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)

System Requirements

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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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Package Archives

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

Source Package MetCirc_1.24.0.tar.gz

Windows Binary MetCirc_1.24.0.zip

macOS 10.13 (High Sierra) MetCirc_1.24.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/MetCirc

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MetCirc

Bioc Package Browser https://code.bioconductor.org/browse/MetCirc/

Package Short Url https://bioconductor.org/packages/MetCirc/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.14 Source Archive