Index

_

_Ontology (class in pyhpo)

A

add() (HPOSet method)

all_genes() (HPOSet method) all_parents (HPOTerm attribute)

B

batch_disease_enrichment() (in module pyhpo.helper) batch_gene_enrichment() (in module pyhpo.helper) batch_omim_disease_enrichment() (in module pyhpo.helper)

batch_orpha_disease_enrichment() (in module pyhpo.helper) batch_set_similarity() (in module pyhpo.helper) batch_similarity() (in module pyhpo.helper)

C

categories (HPOTerm attribute) child_nodes() (HPOSet method) child_of() (HPOTerm method) children (HPOTerm attribute)

combinations() (in module pyhpo.HPOSet) combinations_one_way() (in module pyhpo.HPOSet) common_ancestors() (HPOTerm method) count_parents() (HPOTerm method) custom (InformationContent attribute)

E

enrichment() (EnrichmentModel method)

EnrichmentModel (class in pyhpo.stats)

F

from_bytes() (in module pyhpo.HPOSet) from_disease() (in module pyhpo.HPOSet) from_gene() (in module pyhpo.HPOSet)

from_omim_disease() (in module pyhpo.HPOSet) from_orpha_disease() (in module pyhpo.HPOSet) from_queries() (in module pyhpo.HPOSet) from_serialized() (in module pyhpo.HPOSet)

G

Gene (class in pyhpo) gene (InformationContent attribute) genes (_Ontology attribute) (HPOTerm attribute)

get() (Gene method) (Omim method) (Orpha method) get_hpo_object() (_Ontology method)

H

hpo (Gene attribute) (Omim attribute) (Orpha attribute) hpo() (_Ontology method)

hpo_set() (Gene method) (Omim method) (Orpha method) HPOSet (class in pyhpo) HPOTerm (class in pyhpo)

I

id (Gene attribute) (HPOTerm attribute) (Omim attribute) (Orpha attribute)

information_content (HPOTerm attribute) information_content() (HPOSet method) InformationContent (class in pyhpo.types) is_obsolete (HPOTerm attribute)

L

linkage() (in module pyhpo.stats)

M

match() (_Ontology method)

N

name (Gene attribute) (HPOTerm attribute) (Omim attribute) (Orpha attribute)

O

Omim (class in pyhpo) omim (InformationContent attribute) omim_diseases (_Ontology attribute) (HPOTerm attribute) omim_diseases() (HPOSet method)

Orpha (class in pyhpo) orpha (InformationContent attribute) orpha_diseases (_Ontology attribute) (HPOTerm attribute) orpha_diseases() (HPOSet method)

P

parent_ids() (HPOTerm method) parent_of() (HPOTerm method)

parents (HPOTerm attribute) path() (_Ontology method) path_to_other() (HPOTerm method)

R

remove_modifier() (HPOSet method) replace() (HPOTerm method)

replace_obsolete() (HPOSet method) replaced_by (HPOTerm attribute)

S

search() (_Ontology method) serialize() (HPOSet method) set_custom_information_content() (_Ontology method) shortest_path_to_parent() (HPOTerm method)

shortest_path_to_root() (HPOTerm method) similarity() (HPOSet method) similarity_score() (HPOTerm method) similarity_scores() (HPOSet method) (HPOTerm method)

T

terms() (HPOSet method) to_bytes() (HPOSet method) toJSON() (Gene method) (HPOSet method) (HPOTerm method) (Omim method) (Orpha method)

V

variance() (in module pyhpo.HPOSet)

version() (_Ontology method)