The clusterProfiler package is a versatile tool for enrichment analysis. It is developed within the Bioconductor ecosystem and has become an essential part of this ecosystem. Currently there are more than 30 R packages that rely on clusterProfiler to perform functional analysis for different topics, especially for cancer research. GO analysis relies on GO annotation maintained by the community, and the enrichment analysis for genomic regions relies on genomic annotation maintained by UCSC and Ensembl. There are R packages that contain gene set annotation (e.g., msigdbr) and R client libraries for accessing pathway data (e.g., rWikiPathways). These data can be used directly as background annotation in clusterProfiler through the universal interface to characterize the functional profile of omics data. The ORA algorithm is implemented in the DOSE package21 developed in-house, and the GSEA algorithm is implemented in DOSE and fgsea39 packages.
