MetaboSignal

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

Bioconductor version: Release (3.17)

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	1.30.2
In Bioconductor since	BioC 3.4 (R-3.3) (7 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
Linking To
Suggests	RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown
System Requirements
Enhances
URL

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	MetaboSignal_1.30.2.tar.gz
Windows Binary	MetaboSignal_1.30.2.zip
macOS Binary (x86_64)	MetaboSignal_1.30.2.tgz
macOS Binary (arm64)	MetaboSignal_1.30.2.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 3.17	Source Archive