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ontologySimilarity (version 2.9)

Calculating Ontological Similarities

Description

Calculate similarity between ontological terms and sets of ontological terms based on term information content and assess statistical significance of similarity in the context of a collection of terms sets - Greene et al. 2017 .

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Version

Install

install.packages('ontologySimilarity')

Monthly Downloads

289

Version

2.9

License

GPL (>= 2)

Maintainer

Daniel Greene

Last Published

February 1st, 2026

Functions in ontologySimilarity (2.9)

get_profile_sims

Get similarities of term sets to profile
get_asym_sim_grid

Get asymmetrical similarity matrix
get_sim_grid

Get similarity matrix of pairwise similarities of term sets.
get_sim

Calculate the group similarity of a set of row/column indices
create_sim_index

Create similarity index for list of term sets
get_sim_p

Get similarity p-value
GO_IC

Gene Ontology terms information content.
get_sim_p_from_ontology

Get similarity p-value for subgroup term sets
descendants_IC

Get information content based on number of descendants each term has
get_similarity_rank_matrix

Get matrix of similarity rank from similarity matrix
get_term_sim_mat

Get term-term similarity matrix
ontologySimilarity-package

Functions for Calculating Ontological Similarities
resnik

Calculate Resnik similarity score of two term sets
lin

Calculate Lin similarity score of two term sets
sample_group_sim

Draw sample of group similarities
gene_GO_terms

Gene Ontology annotation of genes
sample_group_sim_from_ontology

Draw sample of group similarities
group_term_enrichment

Identify enriched terms in subgroup
get_term_set_to_term_sims

Get `term sets to term' similarity matrix