clusterProfiler 4.0 contains several new features, including the tidy interface and the compatibility of using ggplot2 for visualization. There is no API change for functional enrichment analyses, and this version is fully compatible with downstream packages (Table S1). After long-term maintenance, clusterProfiler is mature and unlikely to introduce significant API changes in future development. In the event of an API change, we will maintain backward compatibility for at least 1 year and provide a warning message about the change. The clusterProfiler library is freely available at https://www.bioconductor.org/packages/clusterProfiler. The development version of clusterProfiler is hosted on GitHub (https://github.com/YuLab-SMU/clusterProfiler), with many active users. A complete reference of the package suite (Figure 6) is available in the online book, https://yulab-smu.top/biomedical-knowledge-mining-book/, with many examples and detailed explanations on biological knowledge mining. Source codes to reproduce Figures 1, 2, 3, 4, and 5, as well as detailed information about the datasets used in the examples, are available in supplemental information. The clusterProfiler library is one of the popular tools used in functional enrichment analysis (more than 2,500 citations in 2020 according to Google Scholar), and
