This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

MetCirc

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

Bioconductor version: Release (3.17)

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 "4.3") 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

Details

biocViews MassSpectrometry, Metabolomics, ShinyApps, Software, Visualization
Version 1.30.0
In Bioconductor since BioC 3.4 (R-3.3) (7 years)
License GPL (>= 3)
Depends R (>= 3.5), amap (>= 0.8), circlize (>= 0.3.9), scales (>= 0.3.0), shiny (>= 1.0.0), Spectra(>= 1.4.3)
Imports ggplot2 (>= 3.2.1), MsCoreUtils(>= 1.9.2), S4Vectors(>= 0.22.0)
Linking To
Suggests BiocGenerics, graphics (>= 3.5), grDevices (>= 3.5), knitr (>= 1.11), testthat (>= 2.2.1)
System Requirements
Enhances
URL
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package MetCirc_1.30.0.tar.gz
Windows Binary MetCirc_1.30.0.zip
macOS Binary (x86_64) MetCirc_1.30.0.tgz
macOS Binary (arm64) MetCirc_1.30.0.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