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 'minval' 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.