MetCirc
This is thereleased version of MetCirc; for the devel version, seeMetCirc.
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics data
Bioconductor version: Release (3.22)
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("MetCirc")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("MetCirc")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text |
Details
| biocViews | MassSpectrometry,Metabolomics,ShinyApps,Software,Visualization |
| Version | 1.40.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (9 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 |
See More
| Suggests | BiocGenerics, graphics (>= 4.4), grDevices (>= 4.4),knitr (>= 1.48),testthat (>= 3.2.1.1) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | MetCirc_1.40.0.tar.gz |
| Windows Binary (x86_64) | MetCirc_1.40.0.zip |
| macOS Binary (x86_64) | MetCirc_1.40.0.tgz |
| macOS Binary (arm64) | MetCirc_1.40.0.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 |