Genome-scale Metabolic Modeling of CRC-associated Macrophage subtypes Existing Toolboxes Needed: Cobra Toolbox (https://github.com/opencobra) REDGEM and REDHUMAN (https://github.com/EPFL-LCSB) PageRank Analysis (https://www.nature.com/articles/s41540-018-0067-y) REDGEM pipeline seems to work best with TOMLAB, but is not necessary (https://tomopt.com/tomlab/)
Use "GenerateCohort_MacrophageModels" to make the set of models, using the different techniques. All but CORDA are included with the CobraToolbox (https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004808)
The "M1_xxxx" and "M2_xxxx" files are the resulting models The "redHUMAN_xxx" files are the consolidated M1 and M2 models, built using REDHUMAN
Model analyses can be performed with the "AnalysesMacrophageModels" file