MetCirc
This is the development version of MetCirc; for the stable release version, see MetCirc.
Navigating mass spectral similarity in high-resolution MS/MS metabolomics data metabolomics data
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | ||
| NEWS | Text |
Details
| biocViews | MassSpectrometry, Metabolomics, ShinyApps, Software, Visualization |
| Version | 1.43.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (10 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
Follow Installation instructions to use this package in your R session.
| Source Package | MetCirc_1.43.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | MetCirc_1.43.0.tgz |
| macOS Binary (sonoma-arm64) | MetCirc_1.43.0.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 |