Phenotypes comparison based on a pathway consensus approach. Assess the relationship between candidate genes and a set of phenotypes based on additional genes related to the candidate (e.g. Pathways or network neighbors).
|Author||Matthew Page and Patrice Godard|
|Date of publication||None|
|Maintainer||Matthew Page <firstname.lastname@example.org> and Patrice Godard <email@example.com>|
|License||CC BY-NC-ND 4.0|
calcHpSim: Compare HP terms based on semantic similarity
compareHPSets: Compare 2 sets of HP terms based on semantic similarity
computeHpIC: Compute Information Content (IC) for each HP based on genes...
geneByHp: Entrez gene IDs associated to HP terms (Example data)
geneByTrait: Gene associated to trait (Example data)
geneDef: Description of genes (Example data)
hp_ancestors: HP ancestors (Example data)
hpByTrait: HP IDs associated to trait (Example data)
hp_class: HP class (Example data)
hpDef: Description of HP terms (Example data)
hp_descendants: HP descendants (Example data)
hpGeneHeatmap: HP to Gene heatmap
hpGeneListComp: HP semantic similarity for a whole gene list.
hpSetCompBestMatch: Best matches between two sets of HP terms
hpSetCompSummary: Global semantic similarity between 2 HP sets
hqStrNw: STRIND database network of Homo sapiens genes (Example data)
hsEntrezByRPath: Homo sapiens entrez gene ID by Reactome pathway (Example...
rPath: Reactome pathways (Example data)
traitDef: Description of Traits (Example data)