Package: ontologySimilarity 2.7

ontologySimilarity: Calculating Ontological Similarities

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 <doi:10.1093/bioinformatics/btw763>.

Authors:Daniel Greene

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ontologySimilarity.pdf |ontologySimilarity.html✨
ontologySimilarity/json (API)

# Install 'ontologySimilarity' in R:
install.packages('ontologySimilarity', repos = c('https://daniel-jg.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • GO_IC - Gene Ontology terms information content.
  • gene_GO_terms - Gene Ontology annotation of genes

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

4.07 score 1 packages 65 scripts 324 downloads 2 mentions 16 exports 2 dependencies

Last updated 8 months agofrom:ab6e42b13c. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 11 2024
R-4.5-win-x86_64OKNov 11 2024
R-4.5-linux-x86_64OKNov 11 2024
R-4.4-win-x86_64OKNov 11 2024
R-4.4-mac-x86_64OKNov 11 2024
R-4.4-mac-aarch64OKNov 11 2024
R-4.3-win-x86_64OKNov 11 2024
R-4.3-mac-x86_64OKNov 11 2024
R-4.3-mac-aarch64OKNov 11 2024

Exports:create_sim_indexdescendants_ICget_asym_sim_gridget_profile_simsget_simget_sim_gridget_sim_pget_sim_p_from_ontologyget_similarity_rank_matrixget_term_set_to_term_simsget_term_sim_matgroup_term_enrichmentlinresniksample_group_simsample_group_sim_from_ontology

Dependencies:ontologyIndexRcpp

ontologySimilarity Examples

Daniel Greene

Rendered fromontologySimilarity-examples.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2024-03-30
Started: 2016-08-06

Using the Gene Ontology data objects

Daniel Greene

Rendered fromontologySimilarity-GO-example.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2024-03-30
Started: 2016-09-09

Introduction to ontologySimilarity

Daniel Greene

Rendered fromontologySimilarity-introduction.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2024-03-30
Started: 2016-08-06

Readme and manuals

Help Manual

Help pageTopics
Functions for Calculating Ontological SimilaritiesontologySimilarity-package ontologySimilarity
Create similarity index for list of term setscreate_sim_index
Get information content based on number of descendants each term hasdescendants_IC
Gene Ontology annotation of genesgene_GO_terms
Get asymmetrical similarity matrixget_asym_sim_grid
Get similarities of term sets to profileget_profile_sims
Calculate the group similarity of a set of row/column indicesget_sim get_sim.default get_sim.integer get_sim.matrix get_sim.numeric get_sim.sim_index
Get similarity matrix of pairwise similarities of term sets.get_sim_grid
Get similarity p-valueget_sim_p get_sim_p.default get_sim_p.integer get_sim_p.matrix get_sim_p.numeric get_sim_p.sim_index
Get similarity p-value for subgroup term setsget_sim_p_from_ontology
Get matrix of similarity rank from similarity matrixget_similarity_rank_matrix
Get `term sets to term' similarity matrixget_term_set_to_term_sims
Get term-term similarity matrixget_term_sim_mat
Gene Ontology terms information content.GO_IC
Identify enriched terms in subgroupgroup_term_enrichment
Calculate Lin similarity score of two term setslin
Calculate Resnik similarity score of two term setsresnik
Draw sample of group similaritiessample_group_sim sample_group_sim.default sample_group_sim.integer sample_group_sim.matrix sample_group_sim.numeric sample_group_sim.sim_index
Draw sample of group similaritiessample_group_sim_from_ontology