Workflow use cases. Examples of workflows that can be easily generated using tools from the ChIPseeqer framework are shown. The starting point is always the result of peak detection: a set of enriched regions/peaks. (A) The aim of the workflow is to analyze a subset of the peaks that have a specific motif. From all the peaks that have the motif, we look for those that bind in the promoters of known genes. Pathways analysis is then performed on these genes in order to reveal enriched pathways associated with this particular subset of peaks. (B) This workflow allows locating and characterizing distal regulatory elements (i.e., intergenic peaks) that overlap with enhancer marks (e.g., H3K4me1 binding), in terms of motifs and conservation. Different workflows can be created using any combination of the ChIPseeqer tools.