gembox

In-house toolbox for genome-scale metabolic modeling (GEM) for the Ruppin lab. This is an R package that implements GEM functionalities.

Provided as is without warranty of any kind.

Current Functions

• Query of metabolic model/network data, and basic manipulations of metabolic models
• FBA, FVA, FCA
• Simulating reaction knockouts; MOMA
• Sampling: ACHR
• Metabolic-EP
• Incorporating gene expression data: iMAT, PRIME, GIMME, E-Fmin, the method of Lee and Smallbone, and their variations
• MTA, rMTA and their variations
• Differential flux analysis and metabolic pathway enrichment analysis
• Visualization of metabolic network and differential flux results

Dependencies

• ILOG CPLEX Optimization Studio or Gurobi (free academic licenses available)
• R packages
  • Depends: Matrix, data.table
  • Imports: stringr, parallel, pbmcapply
  • LinkingTo: Rcpp, RcppArmadillo
  • Suggests: Rcplex2 (ruppinlab/Rcplex2), gurobi, R.matlab, sybilSBML, rlist, fgsea, igraph, ggplot2, RColorBrewer, visNetwork, hypergraph, hyperdraw
  • At least one of Rcplex2 (ruppinlab/Rcplex2) and gurobi is required for running optimizations

This package for now only works on Linux and MacOS.