README.md

In DikshantPradhan/FluxCouplingTools:

FluxCouplingTools

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

DikshantPradhan/FluxCouplingTools documentation built on Aug. 27, 2019, 2:19 a.m.