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 <p>Users familiar with R/Bioconductor have several R packages to perform epigenomic enrichment analysis. <strong>ChIPseeker</strong> (Yu et al., 2015) provides a variety of functions for annotating user-provided ROIs in BED format by proximity to the nearby genes, finding overlaps with epigenomic regions, performing gene-centric and epigenomic enrichment analysis. <strong>ChIPseeker</strong> employs permutation strategy to calculate overlap enrichment p-values. <strong>ChIPseeker</strong> provides access to multi-organism epigenomic datasets from GEO (Gene Expression Omnibus), expanding enrichment analysis to species other than human. Coupled with excellent visualization capabilities, <strong>ChIPseeker</strong> is a well-designed tool with complete functionality for the interpretation of genome-wide ROIs.</p>
 <p>&ndash; Excerpt from the article: <a href="https://academic.oup.com/bioinformatics/article/33/20/3323/3892391"  class="external-link" target="_blank" rel="noopener">Epigenomic annotation-based interpretation of genomic data: from enrichment analysis to machine learning</a>, <strong><em>Bioinformatics</em></strong>, 2017, 33(20):3323-3330.</p>
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