├── Functions ├── DietConstrain.m ├── GenerateMSPInformation.m ├── KeepNecessaryRxns.m ├── MakeCommunity.m ├── MetaGenomicsReactionScore.m ├── MetagenomeToReactions.m ├── ReactionAbundanceGenerator.m ├── ReactobiomeGenerator.m ├── RxnRichnessGenerator.m ├── USDAcreatingDiet.m ├── checkCatalog.m ├── contextSpecificModelGenertion.m ├── contextSpecificModelTune.m ├── convertCatalogAnnotation.m ├── fakeModelGenerator.m ├── microbiomeGEMgeneration.m └── pRSEGenerator.m ├── MIGRENE_pipeline.m ├── README.md ├── data ├── BacterialAbundance.xlsx ├── MSPgeneProfile.txt ├── SubSet_hs_10_4_igc2_annot.txt ├── Taxonomy.xlsx ├── ec2rn.txt ├── ko2rn.txt └── pathways.xlsx ├── mat ├── DietInput.mat ├── Diets.mat ├── KBase.mat ├── MetInformation.mat ├── RefMetabolicModel.mat ├── USDAdataset.mat ├── bibliome.mat └── microbiomeGEM.mat ├── saveDir └── test.txt └── tutorials ├── IntegrationCatalogToModel.m ├── MAGMAgeneration.m └── PersonalizedMicrobiomeMetabolism.m /Functions/DietConstrain.m: 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