CommunityProfiling

Community profiling (CP) is a guilt-by-association approach for predicting functional associations between proteins: two proteins are predicted to be associated if they share similar presence and absence profiles (called community profiles) across microbial communities. Community profiling is conceptually similar to the phylogenetic profiling approach to functional prediction, however with fundamental differences. This package provides different profile construction methods and correlation metrics, which we have shown are important for optimizing the performance of this new approach.

Please refer to our paper for details of the algorithm:
Dazhi Jiao, Wontack Han and Yuzhen Ye. Functional association prediction by community profiling. Methods, 2017