PyHPO
3.1.4
API documentation:
HPOTerm
Ontology
Annotations
HPOSet
Statistics
Similarity
Matrix
Handling master data
Parser
PyHPO
Index
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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R
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S
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T
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V
_
__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 (pyhpo.term.InformationContent attribute)
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
gene (pyhpo.term.InformationContent attribute)
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
hpo (pyhpo.annotations.DiseaseSingleton attribute)
(pyhpo.annotations.GeneSingleton attribute)
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() (in module pyhpo.parser.generics)
information_content (pyhpo.term.HPOTerm attribute)
information_content() (pyhpo.set.HPOSet method)
InformationContent (class in pyhpo.term)
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)
negative_hpo (pyhpo.annotations.DiseaseSingleton attribute)
O
omim (pyhpo.term.InformationContent attribute)
omim_diseases (pyhpo.ontology.OntologyClass attribute)
(pyhpo.term.HPOTerm attribute)
omim_diseases() (pyhpo.set.HPOSet method)
omim_excluded_diseases (pyhpo.ontology.OntologyClass attribute)
OntologyClass (class in pyhpo.ontology)
orpha (pyhpo.term.InformationContent attribute)
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_obo_section() (in module pyhpo.parser.obo)
path() (pyhpo.ontology.OntologyClass method)
path_to_other() (pyhpo.term.HPOTerm method)
R
remove_modifier() (pyhpo.set.HPOSet method)
remove_outcommented_rows() (in module pyhpo.parser.generics)
replace_obsolete() (pyhpo.set.HPOSet method)
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 (pyhpo.annotations.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)
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)