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 example, the Gene Ontology Meta Annotator for Plants (GOMAP) is optimized for GO annotation of large, repetitive plant genomes.40 Users can develop a pipeline to combine GOMAP with clusterProfiler to characterize the functionality of sequencing data from plant species, including wheat, maize, soy, and rice. The clusterProfiler library has been incorporated into different pipelines, such as TCGA Workflow,12 recount workflow,41 RNASeqR,42 and MAGeCKFlute.43
