Chapter 14 Motif and Feature Enrichment with ArchR

After identification of a robust peak set, we often want to predict what transcription factors may be mediating the binding events that create those accessible chromatin sites. This can be helpful in assessing marker peaks or differential peaks to understand if these groups of peaks are enriched for binding sites of specific transcription factors. For example, we often find enrichment of key lineage-defining TFs in cell type-specific accessible chromatin regions. In a similar fashion, we might want to test various groups of peaks for enrichment of other known features. For example, we might want to know if cell type-specific ATAC-seq peaks for cell type A are enriched for another set of genomic regions such as ChIP-seq peaks. This chapter details how these enrichments are performed in ArchR.