All functions

add_ancestor() add_death() add_disease_genes() add_evidence() add_gene_frequency() add_genes() add_gpt_annotations() add_hpo_definition() add_hpo_id() add_hpo_name() add_info_content() add_mondo() add_ndisease() add_omop() add_onset() add_ont_lvl() add_pheno_frequency() add_prevalence() add_severity() add_tier()

Add functions

add_disease()

Add diseases

disease_id_to_omop

Human Phenotype Ontology: Disease ID to OMOP

disease_map

Human Phenotype Ontology: Disease ID to Disease Name and Disease Description

filter_descendants()

Filter functions

get_hpo() get_hpo_id_direct() get_mappings()

Get functions

get_gene_lists()

Get gene list

get_top_phenos()

Get top phenotypes

gpt_annot_check()

Check annotations from GPT

gpt_annot_class()

GPT annotations: add severity class

gpt_annot_codify()

Check annotations from GPT

gpt_annot_melt()

Melt annotations from GPT

gpt_annot_plot()

Plot annotations from GPT

gpt_annot_plot_branches()

Plot annotations from GPT: by branch

gpt_annot_read()

Read annotations from GPT

hpo_api()

HPO API

hpo_deaths

Human Phenotype Ontology: Age of Death

hpo_frequencies

Human Phenotype Ontology: phenotype frequencies

hpo_id_to_omop

Human Phenotype Ontology: HPO ID to OMOP

hpo_modifiers

Human Phenotype Ontology: disease modifiers

hpo_onsets

Human Phenotype Ontology: disease onset

hpo_tiers

Human Phenotype Ontology: disease severity tiers

hpo_tiers_auto

Human Phenotype Ontology: disease severity tiers (auto)

hpo_to_matrix()

HPO to matrix

list_columns()

List columns

load_phenotype_to_genes()

Load phenotype_to_genes

annotate_phenos() example_phenos()

Main functions

make_igraph_object() make_network_object() make_network_plot() make_phenos_dataframe() make_tiers()

Make functions

list_deaths() list_onsets()

Map functions

map_disease()

Map disease

map_phenotypes()

Harmonise phenotypes

newlines_to_definition()

Add new lines to disease description

per_branch_plot()

Plot N phenotypes per branch

phenos_to_granges()

Phenotypes to GenomicRanges

plot_arrow()

Plot arrow

plot_evidence()

Plot evidence

plot_top_phenos()

Plot top phenotypes

search_hpo()

Search the Human Phenotype Ontology