Index

_

__call__() (pyhpo.similarity.base.SimilarityBase method)

A

add_decipher_to_term() (in module pyhpo.parser.diseases) add_gene_to_term() (in module pyhpo.parser.genes) add_negative_decipher_to_term() (in module pyhpo.parser.diseases) add_negative_omim_to_term() (in module pyhpo.parser.diseases) add_negative_orpha_to_term() (in module pyhpo.parser.diseases) add_omim_to_term() (in module pyhpo.parser.diseases)

add_orpha_to_term() (in module pyhpo.parser.diseases) all_decipher_diseases() (in module pyhpo.parser.diseases) all_genes() (in module pyhpo.parser.genes) (pyhpo.set.HPOSet method) all_omim_diseases() (in module pyhpo.parser.diseases) all_orpha_diseases() (in module pyhpo.parser.diseases)

B

BasicHPOSet (class in pyhpo.set)

build_ontology_annotations() (in module pyhpo.parser)

C

child_nodes() (pyhpo.set.HPOSet method) child_of() (pyhpo.term.HPOTerm method) children (pyhpo.term.HPOTerm attribute) columns (pyhpo.matrix.Matrix attribute)

combinations() (pyhpo.set.HPOSet method) combinations_one_way() (pyhpo.set.HPOSet method) comment (pyhpo.term.HPOTerm attribute) common_ancestors() (pyhpo.term.HPOTerm method) count_parents() (pyhpo.term.HPOTerm method)

D

Decipher (built-in class) decipher (pyhpo.term.InformationContent attribute) Decipher.__call__() (in module pyhpo.annotations.DiseaseDict) Decipher.get() (in module pyhpo.annotations.DiseaseDict) decipher_diseases (pyhpo.term.HPOTerm attribute)

DecipherDisease (built-in class) DecipherDisease.hpo_set() (in module pyhpo.annotations.Annotation) DecipherDisease.toJSON() (in module pyhpo.annotations.Annotation) definition (pyhpo.term.HPOTerm attribute) Distance (class in pyhpo.similarity.defaults)

E

enrichment() (pyhpo.stats.EnrichmentModel method) (pyhpo.stats.HPOEnrichment method)

EnrichmentModel (class in pyhpo.stats)

F

from_queries() (pyhpo.set.HPOSet class method)

from_serialized() (pyhpo.set.HPOSet class method)

G

Gene (built-in class) gene (pyhpo.term.InformationContent attribute) Gene.__call__() (in module pyhpo.annotations.Gene) Gene.get() (in module pyhpo.annotations.Gene) genes (pyhpo.ontology.OntologyClass attribute) (pyhpo.term.HPOTerm attribute)

GeneSingleton (built-in class) GeneSingleton.hpo_set() (in module pyhpo.annotations.Annotation) GeneSingleton.toJSON() (in module pyhpo.annotations.Annotation) get_hpo_object() (pyhpo.ontology.OntologyClass method) GraphIC (class in pyhpo.similarity.defaults)

H

hpo (DecipherDisease attribute) (GeneSingleton attribute) (OmimDisease attribute) (OrphaDisease attribute)

HPOEnrichment (class in pyhpo.stats) HPOSet (class in pyhpo.set) HPOTerm (class in pyhpo.term)

I

id (DecipherDisease attribute) (GeneSingleton attribute) (OmimDisease attribute) (OrphaDisease attribute) (pyhpo.term.HPOTerm attribute)

id_from_string() (in module pyhpo.parser.generics) information_content (pyhpo.term.HPOTerm attribute) information_content() (pyhpo.set.HPOSet method) InformationCoefficient (class in pyhpo.similarity.defaults) InformationContent (class in pyhpo.term)

J

JC (class in pyhpo.similarity.defaults)

L

Lin (class in pyhpo.similarity.defaults)

longest_path_to_bottom() (pyhpo.term.HPOTerm method) longest_path_to_root() (pyhpo.term.HPOTerm method)

M

match() (pyhpo.ontology.OntologyClass method)

Matrix (class in pyhpo.matrix)

N

n_cols (pyhpo.matrix.Matrix attribute) n_rows (pyhpo.matrix.Matrix attribute) name (DecipherDisease attribute) (GeneSingleton attribute) (OmimDisease attribute) (OrphaDisease attribute) (pyhpo.term.HPOTerm attribute)

O

Omim (built-in class) omim (pyhpo.term.InformationContent attribute) Omim.__call__() (in module pyhpo.annotations.DiseaseDict) Omim.get() (in module pyhpo.annotations.DiseaseDict) omim_diseases (pyhpo.ontology.OntologyClass attribute) (pyhpo.term.HPOTerm attribute) omim_diseases() (pyhpo.set.HPOSet method) omim_excluded_diseases (pyhpo.ontology.OntologyClass attribute) OmimDisease (built-in class) OmimDisease.hpo_set() (in module pyhpo.annotations.Annotation)

OmimDisease.toJSON() (in module pyhpo.annotations.Annotation) OntologyClass (class in pyhpo.ontology) Orpha (built-in class) orpha (pyhpo.term.InformationContent attribute) Orpha.__call__() (in module pyhpo.annotations.DiseaseDict) Orpha.get() (in module pyhpo.annotations.DiseaseDict) orpha_diseases (pyhpo.term.HPOTerm attribute) OrphaDisease (built-in class) OrphaDisease.hpo_set() (in module pyhpo.annotations.Annotation) OrphaDisease.toJSON() (in module pyhpo.annotations.Annotation)

P

parent_ids() (pyhpo.term.HPOTerm method) parent_of() (pyhpo.term.HPOTerm method) parents (pyhpo.term.HPOTerm attribute)

parse_obo_section() (in module pyhpo.parser.obo) path() (pyhpo.ontology.OntologyClass method) path_to_other() (pyhpo.term.HPOTerm method)

R

Relevance (class in pyhpo.similarity.defaults) remove_modifier() (pyhpo.set.HPOSet method) remove_outcommented_rows() (in module pyhpo.parser.generics)

replace_obsolete() (pyhpo.set.HPOSet method) Resnik (class in pyhpo.similarity.defaults) rows (pyhpo.matrix.Matrix attribute)

S

search() (pyhpo.ontology.OntologyClass method) serialize() (pyhpo.set.HPOSet method) set_custom() (pyhpo.term.InformationContent method) shortest_path_to_parent() (pyhpo.term.HPOTerm method) shortest_path_to_root() (pyhpo.term.HPOTerm method) similarity() (pyhpo.set.HPOSet method)

similarity_score() (pyhpo.term.HPOTerm method) SimilarityBase (class in pyhpo.similarity.base) symbol (GeneSingleton attribute) synonym (pyhpo.term.HPOTerm attribute) synonym_match() (pyhpo.ontology.OntologyClass method) synonym_search() (pyhpo.ontology.OntologyClass method)

T

terms_from_file() (in module pyhpo.parser.obo)

toJSON() (pyhpo.set.HPOSet method) (pyhpo.term.HPOTerm method)

V

variance() (pyhpo.set.HPOSet method)