gibbslab / exp2flux

An R package to incorporate in a continuous way the gene-expression data as FBA flux boundaries in a metabolic model. Also, functions to calculate and plot the differences between model fluxes in different metabolic scenarios was included. This is an implementation of the algorithm described by Lee et al. (2012) in DOI: 10.1186/1752-0509-6-73.

exp2flux : convert gene EXPression data TO FBA FLUX bounds.

The exp2flux package was designed as a tool to convert EXPression data TO FBA FLUX bounds.

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/exp2flux")
library("exp2flux")

Available functions:

Function	Description
exp2flux	Convert Gene Expression Data to FBA flux bounds
fluxDifferences	Report the fold change of fluxes between two models
plotDifferences	Plot the fold change of fluxes between two models into a bipartite graph

Citation

Daniel Osorio, Kelly Botero, Janneth Gonzalez and Andres Pinzon-Velasco (2016). exp2flux: convert EXPression data to FBA FLUXes. R package version 0.1.