An implementation of the Clique-Extracted Ontology (CliXO) algorithm

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.

Quick Start clixo R

Read vignette for simple example in R

Download R script

Reference manual

References

[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