MetaboSignal

This is the development version of MetaboSignal; for the stable release version, see MetaboSignal.

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


Bioconductor version: Development (3.20)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.35.0
In Bioconductor since BioC 3.4 (R-3.3) (8 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
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Suggests RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown
Linking To
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Depends On Me
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Build Report Build Report

Package Archives

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

Source Package MetaboSignal_1.35.0.tar.gz
Windows Binary MetaboSignal_1.35.0.zip
macOS Binary (x86_64) MetaboSignal_1.35.0.tgz
macOS Binary (arm64) MetaboSignal_1.35.0.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