add_annotation	add_annotation
all_group_sim_methods	all_methods
all_term_IC_methods	all_methods
all_term_sim_methods	all_methods
alternative_GO_terms	create_ontology_DAG_from_GO_db
annotated_terms	annotation
avg_children	n_terms
avg_parents	n_terms
CA_terms	common_ancestor
create_ontology_DAG	create_ontology_DAG
create_ontology_DAG_from_GO_db	create_ontology_DAG_from_GO_db
create_ontology_DAG_from_igraph	create_ontology_DAG_from_igraph
dag_add_random_children	dag_random
dag_all_terms	dag_all_terms
dag_ancestors	dag_terms
dag_as_dendrogram	dag_treelize
dag_as_DOT	dag_viz
dag_as_igraph	dag_as_igraph
dag_children	dag_terms
dag_circular_viz	dag_viz
dag_depth	dag_depth
dag_distinct_ancestors	dag_distinct_ancestors
dag_enrich_on_genes	dag_enrich_on_items
dag_enrich_on_items	dag_enrich_on_items
dag_enrich_on_offsprings	dag_enrich_on_offsprings
dag_enrich_on_offsprings_by_permutation	dag_enrich_on_offsprings_by_permutation
dag_filter	dag_filter
dag_graphviz	dag_viz
dag_has_terms	dag_has_terms
dag_height	dag_depth
dag_is_leaf	dag_root
dag_leaves	dag_root
dag_longest_dist_from_ancestors	dag_longest_dist_to_offspring
dag_longest_dist_to_offspring	dag_longest_dist_to_offspring
dag_n_leaves	dag_all_terms
dag_n_relations	dag_all_terms
dag_n_terms	dag_all_terms
dag_offspring	dag_terms
dag_parents	dag_terms
dag_permutate_children	dag_reorder
dag_random	dag_random
dag_random_tree	dag_random
dag_reorder	dag_reorder
dag_root	dag_root
dag_shiny	dag_shiny
dag_shortest_dist_from_ancestors	dag_longest_dist_to_offspring
dag_shortest_dist_from_root	dag_depth
dag_shortest_dist_to_leaves	dag_depth
dag_shortest_dist_to_offspring	dag_longest_dist_to_offspring
dag_siblings	dag_terms
dag_treelize	dag_treelize
group_sim	group_sim
has_annotation	n_annotations
import_obo	import_obo
import_ontology	import_obo
import_owl	import_obo
import_ttl	import_obo
LCA_depth	common_ancestor
LCA_term	common_ancestor
longest_distances_directed	distance
longest_distances_via_LCA	distance
max_ancestor_id	common_ancestor
max_ancestor_path_sum	common_ancestor
max_ancestor_v	common_ancestor
mcols,ontology_DAG-method	mcols_ontology_DAG
mcols<-,ontology_DAG-method	mcols_ontology_DAG
method_param	method_param
MICA_IC	common_ancestor
MICA_term	common_ancestor
NCA_term	common_ancestor
n_ancestors	n_terms
n_annotations	n_annotations
n_children	n_terms
n_connected_leaves	n_terms
n_offspring	n_terms
n_parents	n_terms
ontology_chebi	ontology
ontology_DAG	ontology_DAG-class
ontology_DAG-class	ontology_DAG-class
ontology_go	ontology
ontology_hp	ontology
ontology_kw	ontology
ontology_pw	ontology
ontology_rdo	ontology
ontology_vt	ontology
partition_by_level	partition_by_level
partition_by_size	partition_by_level
print.ontology_tree	dag_treelize
print.print_source	print.print_source
random_items	random_terms
random_terms	random_terms
shortest_distances_directed	distance
shortest_distances_via_NCA	distance
show,ontology_DAG-method	show-ontology_DAG-method
simona_opt	simona_opt
term_annotations	annotation
term_IC	term_IC
term_sim	term_sim
[,ontology_DAG,ANY,ANY,ANY-method	subset
[,ontology_DAG,ANY,ANY,missing-method	subset
[,ontology_DAG,ANY,missing,ANY-method	subset
[,ontology_DAG,ANY,missing,missing-method	subset
[,ontology_DAG,missing,ANY,ANY-method	subset
[,ontology_DAG,missing,ANY,missing-method	subset
[,ontology_DAG,missing,missing,ANY-method	subset
[,ontology_DAG,missing,missing,missing-method	subset
[[,ontology_DAG,character,missing-method	subset
