peak-annotation

What problem does it solve?

This Skill helps researchers assign biological meaning to ENCODE peak datasets by annotating peaks with genomic features and functional annotations, facilitating downstream analysis.

Core Features & Use Cases

• Genomic Feature Annotation: Classify peaks into promoter, intron, exon, intergenic, and other categories using tools like ChIPseeker.
• Functional Enrichment Analysis: Perform gene ontology and pathway enrichment on peak-associated genes via tools like clusterProfiler and GREAT.
• Use Case: A researcher has ENCODE H3K27ac peaks from pancreatic tissue and wants to identify enriched biological processes and regulatory features associated with these peaks for disease research.

Quick Start

Load your ENCODE peak file in BED format, annotate peaks with genomic features using ChIPseeker, and then perform GO enrichment on nearby genes with R packages.