Analysis semantic similarity between HPO terms and HPO-based phenotypic similarity between genes and between diseases.

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Documentation for package ‘HPOSim’ version 1.2

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HPOSim-package HPOSim package
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
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 Similarity matrix for two sets 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