Index

_

_index (pyhpo.term.HPOTerm attribute)

A

all_genes() (pyhpo.set.HPOSet method)

all_parents (pyhpo.term.HPOTerm attribute)

B

BasicHPOSet (class in pyhpo.set)

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_diseases (pyhpo.term.HPOTerm attribute) definition (pyhpo.term.HPOTerm attribute)

DiseaseDict (class in pyhpo.annotations) DiseaseSingleton (class in pyhpo.annotations)

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

GeneDict (class in pyhpo.annotations) genes (pyhpo.ontology.OntologyClass attribute) (pyhpo.term.HPOTerm attribute)

GeneSingleton (class in pyhpo.annotations) get_hpo_object() (pyhpo.ontology.OntologyClass method)

H

hierarchy() (pyhpo.term.HPOTerm method) hpo (pyhpo.annotations.DiseaseSingleton attribute) (pyhpo.annotations.GeneSingleton attribute)

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

I

id (pyhpo.annotations.DiseaseSingleton attribute) (pyhpo.annotations.GeneSingleton attribute) (pyhpo.term.HPOTerm attribute) id_from_string() (pyhpo.term.HPOTerm static method)

information_content (pyhpo.term.HPOTerm attribute) information_content() (pyhpo.set.HPOSet method) is_a (pyhpo.term.HPOTerm attribute) is_modifier (pyhpo.term.HPOTerm attribute) is_obsolete (pyhpo.term.HPOTerm attribute)

L

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 (pyhpo.annotations.DiseaseSingleton attribute) (pyhpo.annotations.GeneSingleton attribute) (pyhpo.term.HPOTerm attribute)

O

omim_diseases (pyhpo.ontology.OntologyClass attribute) (pyhpo.term.HPOTerm attribute) omim_diseases() (pyhpo.set.HPOSet method)

omim_excluded_diseases (pyhpo.ontology.OntologyClass attribute) (pyhpo.term.HPOTerm attribute) OntologyClass (class in pyhpo.ontology) orpha_diseases (pyhpo.term.HPOTerm attribute)

P

parent_ids() (pyhpo.term.HPOTerm method) parent_of() (pyhpo.term.HPOTerm method) parents (pyhpo.term.HPOTerm attribute) parse_pheno_file() (in module pyhpo.annotations)

parse_synonym() (pyhpo.term.HPOTerm static method) path() (pyhpo.ontology.OntologyClass method) path_to_other() (pyhpo.term.HPOTerm method) print_hierarchy() (pyhpo.term.HPOTerm method)

R

remove_modifier() (pyhpo.set.HPOSet method) remove_outcommented_rows() (in module pyhpo.annotations)

replace_obsolete() (pyhpo.set.HPOSet method) replaced_by (pyhpo.term.HPOTerm attribute) rows (pyhpo.matrix.Matrix attribute)

S

search() (pyhpo.ontology.OntologyClass method) serialize() (pyhpo.set.HPOSet 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) symbol (pyhpo.annotations.GeneSingleton attribute) synonym (pyhpo.term.HPOTerm attribute) synonym_match() (pyhpo.ontology.OntologyClass method) synonym_search() (pyhpo.ontology.OntologyClass method)

T

to_dataframe() (pyhpo.ontology.OntologyClass method) toJSON() (pyhpo.annotations.DiseaseSingleton method) (pyhpo.annotations.GeneSingleton method) (pyhpo.set.HPOSet method) (pyhpo.term.HPOTerm method)

V

variance() (pyhpo.set.HPOSet method)

X

xref (pyhpo.term.HPOTerm attribute)