ppiPre - an R package for predicting protein-protein interactions

Since the existing experimental techniques for identifying protein-protein interactions (PPIs) are expensive and time-consuming, and the results are incomplete and/or noisy, developing computational methods for effectively predicting PPIs is of great importance. Therefore, we develop the R package ppiPre, which predicts PPIs using heterogeneous data sources, including Gene Ontology (GO) annotations, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotations and topological properties of the PPI network. ppiPre supports up to 20 species and provides useful functions for predicting PPIs and calculating semantic and topological similarities between proteins. ppiPre is open source and freely available from http://cran.r-project.org/web/packages/ppiPre).