MetExplore

miom

Constraint-based modeling of metabolism using Mixed Integer Optimization

dexom

Diversity-based enumeration of optimal context-specific metabolic networks

dexom-python

diversity-based enumeration of optimal context-specific metabolic networks using the cobrapy library

met4j

Met4J is an open-source Java library dedicated to the structural analysis of metabolic networks. It also came with a toolbox gathering CLI for several analyses relevant to metabolism-related research.

phnmnl-FingerprintClustering

Performs unsupervised clustering among a metabolic network from a fingerprint

cobratoolbox-lib

COBRA Toolbox without submodules and minor modifications to improve reproducibility

computeDistanceMatrix

container-computeDistanceMatrix

container-PathwayEnrichment

dexom-evaluation

DEXOM submodule with data for evaluation

MetaboliteIDConverter

metexplore2_maintenance

MetExploreViz

phnmnl-PathwayEnrichment

pathway enrichment tool for Docker containerization into Galaxy PhenoMeNal instance

tool-PathwayEnrichment

tool-SBML2MetexploreJsonGraph