MetaboSignal

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4

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

Bioconductor version: Development (3.24)

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")):

Andrea Rodriguez-Martinez, Rafael Ayala, Joram M. Posma, Ana L. Neves, Maryam Anwar, Jeremy K. Nicholson, Marc-Emmanuel Dumas. MetaboSignal: MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways. doi:10.18129/B9.bioc.MetaboSignal, R package version 1.43.0, https://bioconductor.org/packages/MetaboSignal.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneSignaling, GeneTarget, GraphAndNetwork, KEGG, Network, Pathways, Reactome, Software
Version	1.43.0
In Bioconductor since	BioC 3.4 (R-3.3) (10 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

Suggests	RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	MetaboSignal_1.43.0.tar.gz
Windows Binary (x86_64)	MetaboSignal_1.43.0.zip
macOS Binary (big-sur-x86_64)	MetaboSignal_1.43.0.tgz
macOS Binary (sonoma-arm64)	MetaboSignal_1.43.0.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