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| CePa | Centrlity-based Pathway entrichment (CePa) |
| clipper | clipper |
| convertIdentifiersByVector | Convert pathway identifiers |
| DEGraph | Differential Expression of Graph (DEGraph) |
| degtable | Functions to extract and display results |
| degtable.topResult | Functions to extract and display results |
| prs | Pathway regulation score (PRS) |
| prsWeights | Pathway regulation score (PRS) |
| PRS_wrapper | Pathway Regulation Score (PRS) |
| PWEA | PathWay Enrichment Analysis (PWEA) |
| res | Functions to extract and display results |
| res.topResult | Functions to extract and display results |
| SPIA | Signaling Pathway Impact Analysis (SPIA) |
| TAPPA | Topological Analysis of Pathway Phenotype Association (TAPPA) |
| topo.sig | Functions to extract and display results |
| topo.sig.topResult | Functions to extract and display results |
| TopologyGSA | Gene set analysis exploiting the topology of a pathway (TopologyGSA) |