MotifPeeker

MotifPeeker benchmarks epigenomic profiling methods targeting transcription factors where no gold standard reference exists, using motif enrichment as a key metric.

Key Features:

• General Metrics: Overview of peaks-related general metrics for the datasets including FRiP scores, peak widths and motif-summit distances.
• Known Motif Enrichment Analysis: Statistics for the frequency of user-provided motifs enriched in the datasets.
• Motif Discovery Enrichment Analysis: Statistics for the frequency of ab-initio discovered motifs enriched in the datasets and compared with known motifs.

Scientific Applications:

• Epigenomic Profiling Benchmarking: Comparison and analysis of datasets from epigenomic profiling methods using motif enrichment as the benchmark.
• Transcription Factor Target Assessment: Evaluation of epigenomic profiling methods targeting transcription factors in the absence of a gold standard reference.

Methodology:

Minimal input data is analysed through a single function call, with results compiled into an HTML report containing three sections: general metrics, known motif enrichment analysis, and motif discovery enrichment analysis.