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Bioconductor - MetCirc (development version)

MetCirc

This is the development version of MetCirc; for the stable release version, see MetCirc.

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

Bioconductor version: Development (3.22)

MetCirc comprises a workflow to interactively explore high-resolution MS/MS metabolomics data. MetCirc uses the Spectra object infrastructure defined in the package Spectra 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 "4.5") and enter:


if (!require("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")
Details biocViews MassSpectrometry, Metabolomics, ShinyApps, Software, Visualization Version 1.39.0 In Bioconductor since BioC 3.4 (R-3.3) (8.5 years) License GPL (>= 3) Depends R (>= 4.4), amap (>= 0.8), circlize (>= 0.4.16), scales (>= 1.3.0), shiny (>= 1.8.1.1), Spectra(>= 1.15.3) Imports ggplot2 (>= 3.5.1), MsCoreUtils(>= 1.17.0), S4Vectors(>= 0.43.1) System Requirements URL See More Suggests BiocGenerics, graphics (>= 4.4), grDevices (>= 4.4), knitr (>= 1.48), testthat (>= 3.2.1.1) Linking To Enhances 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.

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