ClusterProfiler 4.0 is a powerful tool for functional enrichment analysis of omics data. It supports functional annotation of both coding and non-coding genomic data across thousands of species, using up-to-date gene annotations. The tool provides a universal interface for gene functional annotation from various sources, enabling efficient data interpretation in diverse scenarios. It also offers a tidy interface for data manipulation and visualization, allowing users to analyze and compare datasets from multiple treatments and time points to reveal functional consensus and differences. ClusterProfiler 4.0 has been significantly enhanced compared to its original version, supporting a wide range of organisms, user-provided annotations, and new annotations. It extends the dplyr and ggplot2 packages to provide tidy interfaces for data operation and visualization. Additional features include gene set enrichment analysis and comparison of enrichment results from multiple gene lists. The tool supports functional enrichment analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and provides a universal interface for biomedical gene sets. It allows users to apply all ontologies or pathways curated in diverse databases as background for customized analyses. ClusterProfiler is widely used in the Bioconductor ecosystem and has been incorporated into more than 30 CRAN and Bioconductor packages, several pipelines, and online platforms. ClusterProfiler 4.0 also supports the analysis of genomic regions, including non-coding regions, by linking them to coding genes and performing functional enrichment analysis. It provides a function to associate genomic regions with coding genes through many-to-many mapping, enabling the identification of biological functions of genomic regions. The tool allows the comparison of functional enrichment results from multiple experimental conditions or time points, providing a user-friendly interface for exploring and plotting results. It supports complex experimental designs and enables the identification of functional consensus and differences among different experiments. ClusterProfiler 4.0 also provides a data frame interface for accessing enriched results, allowing easy export of results as CSV files and manipulation of results using data frame operations. It supports a tidy interface for data operation, enabling users to filter and process enriched results using various criteria. The tool also provides visualization using ggplot2, allowing users to generate publication-quality figures to interpret results. It supports various visualization methods, including lollipop charts and bar charts, to visualize enrichment results. ClusterProfiler 4.0 is a versatile tool for enrichment analysis and has been integrated into various pipelines and packages. It is widely used in the biomedical research community and is expected to continue to be a valuable resource for supporting the discovery of mechanistic insights and improving our understanding of health and disease.ClusterProfiler 4.0 is a powerful tool for functional enrichment analysis of omics data. It supports functional annotation of both coding and non-coding genomic data across thousands of species, using up-to-date gene annotations. The tool provides a universal interface for gene functional annotation from various sources, enabling efficient data interpretation in diverse scenarios. It also offers a tidy interface for data manipulation and visualization, allowing users to analyze and compare datasets from multiple treatments and time points to reveal functional consensus and differences. ClusterProfiler 4.0 has been significantly enhanced compared to its original version, supporting a wide range of organisms, user-provided annotations, and new annotations. It extends the dplyr and ggplot2 packages to provide tidy interfaces for data operation and visualization. Additional features include gene set enrichment analysis and comparison of enrichment results from multiple gene lists. The tool supports functional enrichment analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and provides a universal interface for biomedical gene sets. It allows users to apply all ontologies or pathways curated in diverse databases as background for customized analyses. ClusterProfiler is widely used in the Bioconductor ecosystem and has been incorporated into more than 30 CRAN and Bioconductor packages, several pipelines, and online platforms. ClusterProfiler 4.0 also supports the analysis of genomic regions, including non-coding regions, by linking them to coding genes and performing functional enrichment analysis. It provides a function to associate genomic regions with coding genes through many-to-many mapping, enabling the identification of biological functions of genomic regions. The tool allows the comparison of functional enrichment results from multiple experimental conditions or time points, providing a user-friendly interface for exploring and plotting results. It supports complex experimental designs and enables the identification of functional consensus and differences among different experiments. ClusterProfiler 4.0 also provides a data frame interface for accessing enriched results, allowing easy export of results as CSV files and manipulation of results using data frame operations. It supports a tidy interface for data operation, enabling users to filter and process enriched results using various criteria. The tool also provides visualization using ggplot2, allowing users to generate publication-quality figures to interpret results. It supports various visualization methods, including lollipop charts and bar charts, to visualize enrichment results. ClusterProfiler 4.0 is a versatile tool for enrichment analysis and has been integrated into various pipelines and packages. It is widely used in the biomedical research community and is expected to continue to be a valuable resource for supporting the discovery of mechanistic insights and improving our understanding of health and disease.