Known Motif Enrichment Analysis

关于

Enables comprehensive known motif enrichment analysis for genomic peak files such as ChIP-seq and ATAC-seq, as well as gene lists. By leveraging HOMER tools, it identifies the statistical overrepresentation of established transcription factor motifs within specific genomic coordinates or promoter regions. The skill automates the entire workflow—from genome assembly management and chromosome name standardization to the final calculation of fold enrichment and p-values—providing researchers with detailed HTML reports and sequence statistics to uncover the regulatory drivers behind their genomic data.

主要功能

• Detailed statistical reporting including p-values, fold enrichment, and motif logos.
• Support for multiple input formats including BED, narrowPeak, and gene lists.
• Automated enrichment analysis for ChIP-seq and ATAC-seq peak files.
• Integrated genome assembly management for automated installation of reference data.
• 2 GitHub stars
• Automatic standardization of chromosome naming conventions for consistent analysis.

使用场景

• Uncovering regulatory elements in specific genomic regions with prior TF assumptions.
• Analyzing genomic intervals from ChIP-seq experiments for known regulatory motifs.
• Identifying transcription factor enrichment in promoter regions of co-regulated gene sets.