KEGG is an encyclopedia of genes and genomes.19 Molecular functions are represented by networks of interactions and reactions mainly in the form of KEGG pathways and modules. A KEGG module is a collection of manually defined function units. In some situations, KEGG modules have a more straightforward interpretation. Both KEGG pathways and KEGG modules are supported by clusterProfiler. Many software tools that support KEGG analysis have stopped updating since July 2011 when KEGG initiated an academic subscription model for FTP downloading. These tools use relatively old KEGG data, and the result might be inaccurate and misleading. Fortunately, the KEGG web resource is freely available. The clusterProfiler package does not pack any KEGG data. Instead, it queries the latest online KEGG database through web API to perform functional analysis. The advantage of this feature is obvious: it allows clusterProfiler to use up-to-date data and support all the species that have KEGG annotation (more than 6,000 species are listed in http://www.genome.jp/kegg/catalog/org_list.html). Moreover, clusterProfiler supports the KEGG Orthology database and can be used to perform functional characterization of the microbiomes.20
