This repository contains the CachedFCF and FALCON method as well as other tools used in the paper "Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models". This package also requires the following packages:
sybil, parallel, gurobi, dplyr, pryr, data.tree.
A list of coupled reaction sets can be calculated through the following example code:
grb_model <- convert_sybil_to_gurobi(sybil_model) coupling_mtx <- flux_coupling_raptor(grb_model)$coupled sets <- get_list_of_sets_from_mtx(coupling_mtx)
A list of coupled gene and reaction sets can be calculated through the following example code:
falcon_model <- GRB_generate_falcon_model(sybil_model) coupling_mtx <- flux_coupling_raptor(falcon_model)$coupled sets <- get_list_of_sets_from_mtx(coupling_mtx)
Scripts to reproduce the figures in the paper can be found in the Pradhan2019Analysis repository