Pipeline for the statistical testing of cis-pair enrichment
You will need:
- a species genome
- a set of regions of interest such as DHS or peaks from DNase- or ATAC-SEQ for example or promoter regions
- a motif database in meme form (such as Jaspar)
- your gene sets of interest in which you want to find enrichments
The tools offer a wrapper to handle the full pipeline or each step can be run individually if required.