With the increasing availability of genomic sequences, non-coding genomic regions (e.g., cis-regulatory elements, non-coding RNAs, and transposons) have posed a demanding challenge to exploration of their roles in various biological processes.1 Unlike coding genes, non-coding genomic regions are typically not well functionally annotated. Analyzing biological functions of the proximal genes is a common strategy in research on the biological meaning of a set of non-coding genomic regions. Software tools, such as the Genomic Regions Enrichment of Annotations Tool (GREAT),31 are implemented to follow this strategy. However, these tools only support a limited number of species. For example, GREAT is designed for human and mouse only. In addition, many tools only take the host or nearest genes into consideration but ignore long-distance regulations. Our in-house developed package, ChIPseeker,10 is originally designed for chromatin immunoprecipitation (ChIP) peak annotation, comparison, and visualization and has been employed to analyze genome-wide ROIs, such as open chromatin regions obtained by DNase-seq32 and ATAC-seq.33 To facilitate biological interpretation of genome-wide regions, we implemented a function, seq2gene, in ChIPseeker to associate genomic regions with coding genes through many-to-many
