MetCirc

This is the released version of MetCirc; for the devel version, see MetCirc.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4

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

Bioconductor version: Release (3.23)

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")):

Thomas Naake, Johannes Rainer and Emmanuel Gaquerel. MetCirc: Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics data. doi:10.18129/B9.bioc.MetCirc, R package version 1.42.0, https://bioconductor.org/packages/MetCirc.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	MassSpectrometry, Metabolomics, ShinyApps, Software, Visualization
Version	1.42.0
In Bioconductor since	BioC 3.4 (R-3.3) (10 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

Suggests	BiocGenerics, graphics (>= 4.4), grDevices (>= 4.4), knitr (>= 1.48), testthat (>= 3.2.1.1)
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Build Report	Build Report, r-universe

Package Archives

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

Source Package	MetCirc_1.42.0.tar.gz
Windows Binary (x86_64)	MetCirc_1.41.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	MetCirc_1.42.0.tgz
macOS Binary (sonoma-arm64)	MetCirc_1.42.0.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