fcScan

fcScan identifies clusters of genomic sites within DNA sequences using user-defined criteria to detect combinations of homotypic and heterotypic sites for applications such as cis-regulatory module detection and mutation-enriched locus discovery.

Key Features:

• Implementation: Implemented as an R/Bioconductor package for integration with Bioconductor workflows.
• User-Defined Clustering Criteria: Allows specification of cluster size, inter-cluster distances, and the order and orientation of sites.
• Input Formats: Accepts GRanges, data frame, and VCF/BED file formats.
• Scalability: Performs clustering on vectorized data and is optimized to handle millions of sites from large-scale datasets.
• Cis-Regulatory Module Detection: Detects combinations of transcription factor binding sites within a defined window size to identify cis-regulatory modules.
• Mutation-Enriched Loci Detection: Identifies genomic loci enriched for mutations.
• Flexibility: Parameterizable searches enable tailoring to specific biological questions.

Scientific Applications:

• Cis-regulatory module analysis: Detects combinatorial arrangements of transcription factor binding sites within defined windows to study gene regulation.
• Mutation-enriched locus identification: Locates genomic regions with elevated mutation density for variant impact studies.
• Large-scale NGS data analysis: Applies clustering to millions of sites derived from next-generation sequencing datasets.

Methodology:

Searches for clusters using a grammar-based approach with user-defined grammatical rules and performs clustering on vectorized data using criteria such as cluster size, inter-site distances, order, and orientation.