MetaboSignal

DOI: 10.18129/B9.bioc.MetaboSignal    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see MetaboSignal.

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

Bioconductor version: 3.9

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 <r.ayala14 at imperial.ac.uk>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	GeneSignaling, GeneTarget, GraphAndNetwork, KEGG, Network, Pathways, Reactome, Software
Version	1.14.0
In Bioconductor since	BioC 3.4 (R-3.3) (3 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
LinkingTo
Suggests	RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown
SystemRequirements
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_1.14.0.tar.gz
Windows Binary	MetaboSignal_1.14.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	MetaboSignal_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MetaboSignal
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MetaboSignal
Package Short Url	https://bioconductor.org/packages/MetaboSignal/
Package Downloads Report	Download Stats