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MetaboSignal

MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways


Bioconductor version: Release (3.18)

MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.

Author: Andrea Rodriguez-Martinez, Rafael Ayala, Joram M. Posma, Ana L. Neves, Maryam Anwar, Jeremy K. Nicholson, Marc-Emmanuel Dumas

Maintainer: Andrea Rodriguez-Martinez <andrea.rodriguez-martinez13 at imperial.ac.uk>, Rafael Ayala <rafaelayalahernandez at gmail.com>

Citation (from within R, enter citation("MetaboSignal")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MetaboSignal")

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("MetaboSignal")
MetaboSignal HTML R Script
MetaboSignal 2: merging KEGG with additional interaction resources HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneSignaling, GeneTarget, GraphAndNetwork, KEGG, Network, Pathways, Reactome, Software
Version 1.32.1
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL-3
Depends R (>= 3.3)
Imports KEGGgraph, hpar, igraph, RCurl, KEGGREST, EnsDb.Hsapiens.v75, stats, graphics, utils, org.Hs.eg.db, biomaRt, AnnotationDbi, MWASTools, mygene
System Requirements
URL
See More
Suggests RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown
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 MetaboSignal_1.32.1.tar.gz
Windows Binary MetaboSignal_1.32.1.zip
macOS Binary (x86_64) MetaboSignal_1.32.1.tgz
macOS Binary (arm64) MetaboSignal_1.32.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/MetaboSignal
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MetaboSignal
Bioc Package Browser https://code.bioconductor.org/browse/MetaboSignal/
Package Short Url https://bioconductor.org/packages/MetaboSignal/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive