MetCirc
This package is for version 3.11 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: 3.11
MetCirc comprises a workflow to interactively explore high-resolution MS/MS metabolomics data. MetCirc uses the Spectrum2 and Spectra 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> and Emmanuel Gaquerel <emmanuel.gaquerel at ibmp-cnrs.unistra.fr>
Maintainer: Thomas Naake <thomasnaake at googlemail.com>
citation("MetCirc")):
Installation
To install this package, start R (version "4.0") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ImmunoOncology, MassSpectrometry, Metabolomics, Software, Visualization |
| Version | 1.18.0 |
| 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(>= 2.10.1) |
| Imports | ggplot2 (>= 3.2.1), S4Vectors(>= 0.22.0) |
| System Requirements | |
| URL |
See More
| Suggests | BiocGenerics, graphics (>= 3.5), grDevices (>= 3.5), knitr (>= 1.11), methods (>= 3.5), RUnit (>= 0.4.32), stats (>= 3.5) |
| 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.
| Source Package | MetCirc_1.18.0.tar.gz |
| Windows Binary | MetCirc_1.18.0.zip |
| macOS 10.13 (High Sierra) | MetCirc_1.18.0.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 3.11 | Source Archive |