The article introduces clusterProfiler, an R package designed for comparing biological themes among gene clusters. The package automates the process of biological-term classification and enrichment analysis, combining analysis and visualization modules into a reusable workflow. It supports three species—human, mouse, and yeast—and can be extended to other species and ontologies. The package is released under the Artistic-2.0 License within the Bioconductor project and is freely available online. The authors demonstrate its application using a breast tumor dataset, showing that it can identify different clusters of differentially expressed genes related to various biological processes. The package is designed to be flexible and user-friendly, making it suitable for biologists analyzing high-throughput data from transcriptomics or proteomics. Future improvements include enhancing semantic similarity, ranking gene similarities, and developing a statistical model for comparing functional profiles.The article introduces clusterProfiler, an R package designed for comparing biological themes among gene clusters. The package automates the process of biological-term classification and enrichment analysis, combining analysis and visualization modules into a reusable workflow. It supports three species—human, mouse, and yeast—and can be extended to other species and ontologies. The package is released under the Artistic-2.0 License within the Bioconductor project and is freely available online. The authors demonstrate its application using a breast tumor dataset, showing that it can identify different clusters of differentially expressed genes related to various biological processes. The package is designed to be flexible and user-friendly, making it suitable for biologists analyzing high-throughput data from transcriptomics or proteomics. Future improvements include enhancing semantic similarity, ranking gene similarities, and developing a statistical model for comparing functional profiles.