peak-annotationlisted

# Peak Annotation of ENCODE Data ## When to Use - User wants to annotate genomic peaks with nearby genes, regulatory features, or functional categories - User asks about "peak annotation", "ChIPseeker", "gene assignment", or "peak-to-gene mapping" - User needs to classify peaks as promoter, enhancer, intronic, intergenic, etc. - User wants to run GO/pathway enrichment on genes near their peaks - Example queries: "annotate my H3K27ac peaks with nearby genes", "what genes are near these ATAC-seq peaks?", "run pathway analysis on peak-associated genes" Help the user annotate ENCODE peak calls with genomic features and functional enrichment. Peak annotation bridges the gap between regulatory elements (peaks) and biological function (genes, pathways). This skill covers two complementary approaches: ChIPseeker for genomic feature annotation and visualization, and GREAT for functional enrichment analysis of non-coding regions. ## Literature Foundation | Reference | Journal | Key Contribution | DOI | Citations | |-----------|---------|-----------------|-----|-----------| | Yu et al. (2015) | Bioinformatics | ChIPseeker: R/Bioconductor package for ChIP peak annotation, comparison, and visualization | [10.1093/bioinformatics/btv145](https://doi.org/10.1093/bioinformatics/btv145) | ~3,200 | | McLean et al. (2010) | Nature Biotechnology | GREAT: Genomic Regions Enrichment of Annotations Tool; assigns biological meaning to cis-regulatory regions using basal+extension gene association