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>

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

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: