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.
- 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
- 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.