ATACgraph

ATACgraph analyzes ATAC-seq data to profile chromatin accessibility and quantify differential accessibility for studies of gene regulation and chromatin dynamics.

Key Features:

• Profiling Accessible Chromatin Regions: Profiles nucleosome-free regions (NFRs) and nucleosome-occupied areas to map chromatin accessibility.
• Differential Accessibility Analysis: Identifies differentially accessible regions between ATAC-seq datasets to detect changes in chromatin structure.
• Cross-genome Applicability: Applies to ATAC-seq data from any genome without built-in species restrictions.
• Peak Quantification from callPeak Outputs: Computes peak abundances between samples using peak BED and BigWig files generated by the callPeak module.

Scientific Applications:

• Gene Regulation: Detects accessibility changes at regulatory elements relevant to transcriptional regulation.
• Epigenetic Analysis: Enables assessment of chromatin-based epigenetic modifications through accessibility profiling.
• Chromatin Dynamics in Cellular Contexts and Disease Models: Compares chromatin accessibility across cell types or disease states to study chromatin dynamics.

Methodology:

Uses peak BED and BigWig files generated by the callPeak module to compute peak abundances between samples.