fcScan

fcScan is an R/ package designed to identify clusters of genomic sites based on user-defined criteria. This tool is handy for discovering cis-regulatory modules characterized by a specific combination of transcription factor binding sites within a defined window size. fcScan supports various input formats, including GRanges, data frames, and VCF/BED files, providing flexibility for different types of genomic data. It allows users to set criteria such as cluster size, inter-cluster distances, and the order and orientation of sites, making it adaptable to specific biological questions. With its ability to handle millions of sites efficiently, fcScan is suitable for analyzing high-throughput data generated by techniques like next-generation sequencing.