MetCirc
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics data
Bioconductor version: 3.24 · Package version: 1.43.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MetCirc")Details
| Maintainer | Thomas Naake <thomasnaake@googlemail.com> |
| Author | Thomas Naake <thomasnaake@googlemail.com>, Johannes Rainer <johannes.rainer@eurac.edu> and Emmanuel Gaquerel <emmanuel.gaquerel@ibmp-cnrs.unistra.fr> |
| License | GPL (>= 3) |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | MassSpectrometry, Metabolomics, ShinyApps, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/MetCirc/ |
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 1.43.0, https://bioconductor.org/packages/MetCirc.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | MetCirc_1.43.0.tar.gz |
| macOS binary (arm64) | MetCirc_1.43.0.tgz |
| macOS binary (x86_64) | MetCirc_1.43.0.tgz |
Dependencies
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)
Suggests: BiocGenerics, graphics (>= 4.4), grDevices (>= 4.4), knitr (>= 1.48), testthat (>= 3.2.1.1)