This package facilitates application of Clique-Extracted Ontology (CliXO) algorithm in R. This algorithm was originally implemented in C++ by Michael Kramer1. The input is a feature similarity matrix, while the output is an ontology source-target-similarity-relation data frame.
Read vignette for simple example in R[1] Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T. Inferring gene ontologies from pairwise similarity data. Bioinformatics, 30: i34-i42. 2014. PMID: 24932003 C++ program