MetCirc

DOI: 10.18129/B9.bioc.MetCirc    

This package is for version 3.9 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: 3.9

MetCirc comprises a workflow to interactively explore high-resolution MS/MS metabolomics data: create an MSP object, a format for MS/MS library data, bin m/z values of precursors, calculate similarity between precursors based on the normalised dot product 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 cos.uni-heidelberg.de>

Maintainer: Thomas Naake <thomasnaake at googlemail.com>

Installation

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

if (!requireNamespace("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")

 

PDF	R Script	Workflow for Metabolomics
PDF		Reference Manual
Text		NEWS

Details

biocViews	ImmunoOncology, MassSpectrometry, Metabolomics, Software, Visualization
Version	1.14.0
In Bioconductor since	BioC 3.4 (R-3.3) (3 years)
License	GPL-2
Depends	R (>= 3.5), amap (>= 0.8), circlize (>= 0.3.9), graphics (>= 3.5), grDevices (>= 3.5), methods (>= 3.5), scales (>= 0.3.0), shiny (>= 1.0.0), stats (>= 3.5)
Imports
LinkingTo
Suggests	BiocGenerics, knitr (>= 1.11)
SystemRequirements
Enhances
URL
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_1.14.0.tar.gz
Windows Binary	MetCirc_1.14.0.zip
Mac OS X 10.11 (El Capitan)	MetCirc_1.14.0.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