| clipper | Dissect the pathway to find the path with the greatest association with phenotype. |
| clipperAllRoots | Dissect the pathway to find the path with the greatest association with phenotype. |
| cliqueMeanTest | Mean test for cliques. |
| cliqueMixedTest | Mean test for cliques. |
| cliquePairedTest | Paired mean test for cliques. |
| cliqueVarianceTest | Variance test for cliques. |
| deleteEdge | Remove an edge from 'graphNel' object. |
| easyClip | Easy clip analysis. |
| easyLook | Summarize clipper output. |
| getGraphEntryGenes | Extract all the possible entry point (genes with no entering edges) from graph. |
| getJunctionTreePaths | Extract the shortest paths along the junction tree of the graph. |
| nameCliques | Generate clique names from their own elements. |
| pathQ | Whole pathway test using qpipf. |
| plotInCytoscape | Plot a pathway graph in Cytoscape highlighting the relevant path. |
| prunePaths | Summarize the paths obtained by clipper according to their similarity. |