ChIPseeker

ChIPseeker annotates ChIP-seq peaks, compares epigenomic datasets, and visualizes peak distributions to infer cooperative regulation and generate biological hypotheses.

Key Features:

• Peak Annotation: Retrieves nearest genes around peaks and annotates genomic regions of peaks.
• Statistical Comparison: Implements statistical methods to estimate significance of overlap among ChIP peak datasets.
• GEO Database Integration: Incorporates 15,000 BED files from GEO database for comparison with user datasets.
• Visualization Functions: Summarizes peak experiment coverage, average profiles and heatmaps of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.
• Chromosomal Coverage Visualization: Visualizes ChIP peaks coverage over chromosomes.

Scientific Applications:

• ChIP-seq Data Analysis: Annotates ChIP peaks and analyzes ChIP-seq data in epigenomic studies.
• Cooperative Regulation Inference: Compares datasets to infer co-regulation or transcription factor complexes.
• Epigenomic Dataset Interpretation: Supports annotation, comparison, visualization, and interpretation of variable epigenomic datasets.
• Functional Analysis: Enables functional analysis of epigenomic datasets.
• Genome-wide Distribution Analysis: Analyzes genome-wide and locus-specific distribution of epigenomic datasets.

Methodology:

ChIPseeker implements functions for data preparation, annotation, comparison, and visualization of epigenomic datasets, including statistical methods for estimating significance of overlap among ChIP peak datasets.