The clusterProfiler library is designed to allow the comparison of functional enrichment results from multiple experimental conditions or multiple time points. With an input of a collection of gene lists, the compareCluster function applies a function (e.g., enricher) with user settings to perform functional enrichment analysis for each of the gene lists and aggregates the results into a single object. Thus, enrichment results of multiple groups are easily explored and plotted together for comparison with a user-friendly interface. Comparing functional profiles can reveal functional consensus and differences among different experiments and helps in identifying differential functional modules in omics datasets. In the updated version, compareCluster provides a new interface supporting a formula that is widely used in R for specifying statistical models; this allows more complicated experimental designs to be supported (e.g., time-course experiment with different treatments). With the infrastructure of clusterProfiler to support a wide range of ontology and pathway annotations and multiple organisms, the comparison can be applied to many circumstances.
