gibbslab / g2f

An R package to find the gaps in metabolic networks, and fill it from the stoichiometric reactions of a reference metabolic reconstruction using a weighting function. Also include the option to download all the set of gene-associated stoichiometric reactions for a specific organism from the KEGG database.

g2f : Find and Fill Gaps in Metabolic Networks

The g2f package was designed as a tool to find and fill gaps in metabolic networks. For a given metabolic network, this package finds the gaps (metabolites not produced or not consumed in any other reaction), and fills it from the stoichiometric reactions of a reference metabolic reconstruction using a weighting function. Also the option to download all the set of gene-associated stoichiometric reactions for a specific organism from the KEGG database http://www.genome.jp/kegg/ is available.

Install:

This package required R version 2.10 or higher. If you are using an older version of R you will be prompted to upgrade when you try to install the package.

For install the latest stable version this package directly from GitHub:

# Install 'devtools' R package
install.packages("devtools")

# Install 'g2f' package
devtools::install_github("gibbslab/g2f")
library("g2f")

Available functions:

Function	Description
additionCost	Calculate the cost of addition of a stoichiometric reaction in a metabolic network
blockedReactions	Identify blocked reactions in a metabolic network
gapFill	Find and fill gaps in a metabolic network
getReference	Download all the set of gene-associated stoichiometric reactions for a specific organism from the KEGG database

Citation

Kelly Botero, Daniel Osorio, Janneth Gonzalez and Andres Pinzon-Velasco (2016). g2f: Find and Fill Gaps in Metabolic Networks. R package version 0.1.

Daniel Osorio, Andres Pinzon-Velasco, Nicolas Mendoza-Mejia, Felipe Rojas-Rodriguez and Janneth Gonzalez (2020). g2f as a Novel Tool to Find and Fill Gaps in Metabolic Networks. R package version 0.1.