Pathway enrichment analysis is an essential step toward identifying biological themes that are most characteristic of high-throughput sequencing data. The clusterProfiler library provides a set of functions to unveil biological functions and pathways. Compared with many other tools that do not update background annotation databases in timely fashion and only support a limited number of organisms, clusterProfiler uses up-to-date biological knowledge of genes and biological processes (GO and KEGG) and supports thousands of organisms. In addition, clusterProfiler provides a universal interface for functional analysis with user-provided annotations. This creates the possibility to apply clusterProfiler on functional characterization of different types of data with different biological knowledge. The tidy interface provided in clusterProfiler harmonizes data structures and workflows and makes it easier for the community to develop modular manipulation, visualization, and analysis methods to supplement the existing ecosystem. clusterProfiler has already been integrated into more than 30 packages to perform functional analysis on data obtained using different techniques, including ATAC-seq, multi-region sequencing (MRS), CRISPR/Cas9 screens, and mass spectrometry (Table S1). The clusterProfiler package can be easily integrated into analysis pipelines. For
