scientific-epigenomics-chromatin

What problem does it solve?

Provides an integrated computational epigenomics pipeline that consolidates ChIP-seq peak calling, ATAC-seq accessibility, DNA methylation analysis, ChromHMM chromatin-state modeling, Hi-C 3D genome structure inference, and motif enrichment into a single workflow, enabling coherent regulatory interpretation from multi-omics data.

Core Features & Use Cases

• ChIP-seq peak calling with MACS2/MACS3
• ATAC-seq nucleosome-free region detection
• DNA methylation pattern analysis (WGBS/RRBS)
• ChromHMM-based chromatin-state modeling
• Hi-C contact maps and TAD detection
• Transcription factor motif enrichment
• Differential binding analysis with DiffBind
• ToolUniverse integration via ChIP-Atlas
• Use Case: multi-omics datasets across samples to annotate regulatory landscapes and compare chromatin states.

Quick Start

Run the integrated epigenomics workflow on ChIP-seq and ATAC-seq data to produce peaks, methylation profiles, chromatin-state annotations, and 3D genome features.