EpiCompare

EpiCompare compares and analyses epigenetic datasets for quality control and benchmarking purposes.

Key Features:

• General Metrics: Computes metrics on peaks (percentage of blacklisted and non-standard peaks, and peak widths) and fragments (duplication rate) of samples.
• Peak Overlap Analysis: Calculates percentage and statistical significance of overlapping and non-overlapping peaks, including upset plot visualization.
• Functional Annotation: Performs functional annotation of peaks using ChromHMM, ChIPseeker and enrichment analysis, including peak enrichment around TSS.
• Integrated Reporting: Outputs all results in a single interactive HTML report combining the three analysis sections.

Scientific Applications:

• Quality Control of Epigenomic Datasets: Evaluates sample quality through peak metrics, fragment duplication rates, and blacklisted peak percentages.
• Benchmarking of Epigenomic Experiments: Compares multiple epigenomic datasets to assess reproducibility and consistency across samples.
• Functional Interpretation of Peaks: Annotates peak sets with chromatin states, genomic features, and enrichment patterns to infer regulatory potential.

Methodology:

EpiCompare combines a variety of downstream analysis tools and requires peak files as input; specific computational algorithms are not explicitly detailed in the sources.