| DOSE-package | Disease Ontology Semantic and Enrichment analysis Implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring DO semantic similarities, and hypergeometric test for enrichment analysis. |
| clusterSim | clusterSim |
| computeIC | compute information content |
| DataSet | Datasets |
| DGN_EXTID2PATHID | Datasets |
| DGN_PATHID2EXTID | Datasets |
| DGN_PATHID2NAME | Datasets |
| DO2ALLEG | Datasets |
| DO2EG | Datasets |
| DOIC | Datasets |
| DOLite2EG | Datasets |
| DOLiteTerm | Datasets |
| DOSE | Disease Ontology Semantic and Enrichment analysis Implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring DO semantic similarities, and hypergeometric test for enrichment analysis. |
| doSim | doSim |
| dotbl | Datasets |
| EG2ALLDO | Datasets |
| EG2DO | Datasets |
| EG2DOLite | Datasets |
| enrichDGN | Enrichment analysis based on the DisGeNET (<URL: http://www.disgenet.org/>) |
| enrichDGNv | enrichDGN |
| enrichDO | DO Enrichment Analysis |
| enricher_internal | enrich.internal |
| enrichMap | enrichMap |
| enrichNCG | enrichNCG |
| enrichResult-class | Class "enrichResult" This class represents the result of enrichment analysis. |
| EXTID2NAME | EXTID2NAME |
| fortify.enrichResult | fortify |
| gene2DO | convert Gene ID to DO Terms |
| geneID | geneID generic |
| geneInCategory | geneInCategory generic |
| geneList | Datasets |
| geneSim | geneSim |
| gseahResult-class | Class "gseaResult" This class represents the result of GSEA analysis |
| gseaResult-class | Class "gseaResult" This class represents the result of GSEA analysis |
| GSEA_internal | GSEA_internal |
| gseDGN | DisGeNET Gene Set Enrichment Analysis |
| gseDO | DO Gene Set Enrichment Analysis |
| gseNCG | NCG Gene Set Enrichment Analysis |
| gsfilter | gsfilter |
| mclusterSim | mclusterSim |
| NCG_EXTID2PATHID | Datasets |
| NCG_PATHID2EXTID | Datasets |
| NCG_PATHID2NAME | Datasets |
| rebuildAnnoData | rebuiding annotation data |
| setReadable | setReadable |
| show | show method |
| show-method | Class "enrichResult" This class represents the result of enrichment analysis. |
| show-method | Class "gseaResult" This class represents the result of GSEA analysis |
| simplot | simplot |
| summary | summary method |
| summary-method | Class "enrichResult" This class represents the result of enrichment analysis. |
| summary-method | Class "gseaResult" This class represents the result of GSEA analysis |
| theme_dose | theme_dose |
| VDGN_EXTID2PATHID | Datasets |
| VDGN_PATHID2EXTID | Datasets |
| VDGN_PATHID2NAME | Datasets |