| bestRanking | Identify the best ranking |
| exprMaguire | Gene expression from Maguire et al. RNA-seq data |
| fitness | Fitness of gene removal-based submodels with different gene rankings |
| iMK735 | iMK735 metabolic models in hypoxia and normoxia |
| metaboGSE | Gene set enrichment analysis |
| pwDesc | Description of gene set IDs |
| relativeExpr | Relative expression data (log2 counts) |
| rescue | Rescue a model |
| rmGenes | Generate a submodel by removing genes |
| scoreGeneDel | Structure of Class "scoreGeneDel" |
| simulateSubmnet | Plot fitness of submodels built by gene removal in a condition |
| submnet | Simulation of gene removal-based submodel series with a given ranking |
| weightReacts | Compute weights of rescue reactions |
| yarli2GO | GO annotation retrieved from Uniprot |
| yarliGSE | Gene set enrichment example for Yarrowia lipolytica |
| yarliSubmnets | Submodel construction example for Yarrowia lipolytica |
| zscoreExpr | Z-score of expression data |