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| HPOSim-package | HPOSim package |
| calcDiseaseTermSim | Semantic Similarity of Two HPO Terms Based on Diseases |
| calcTermSim | Semantic Similarity of Two HPO Terms |
| getDiseaseListSim | Pairwise Similarity for a List of Diseases |
| getDiseaseSim | Phenotype-based similarity for two diseases base on HPO |
| getGeneListSim | Pairwise Similarity for a List of Genes |
| getGeneSim | Phenotype-based similarity for two genes base on HPO |
| getMinimumSubsumer | Get minimum subsumer (MICA) of Two HPO Terms |
| getSimWang | Semantic Similarity Between Two HPO Terms by Wang's Method |
| getTerm | Get information of HPO terms |
| getTermAncestors | Get Ancestors of HPO Terms |
| getTermChildren | Get Direct Children of HPO terms |
| getTermListSim | Get pairwise similarities of a list of HPO terms |
| getTermOffsprings | Get Offspring of HPO terms |
| getTermParents | Get Direct Parents of HPO Terms |
| HPODiseaseEnrichment | HPO enrichment analysis of Disease List |
| HPODiseaseNOASubNetEnrichment | HPO enrichment analysis of disease network using NOA |
| HPODiseaseNOAWholeNetEnrichment | HPO enrichment analysis of disease network using NOA |
| HPOGeneEnrichment | HPO enrichment analysis of Gene List |
| HPOGeneNOASubNetEnrichment | HPO enrichment analysis of gene network using NOA |
| HPOGeneNOAWholeNetEnrichment | HPO enrichment analysis of gene network using NOA |
| HPOSim | HPOSim package |