BaRDIC

BaRDIC calls peaks in RNA-DNA interaction data to detect interactions between chromatin-associated non-coding RNAs and genomic loci from next-generation sequencing (NGS) experiments.

Key Features:

• Bias Correction: Accounts for chromatin heterogeneity and distance-dependent decay of interaction frequency in RNA-DNA interaction datasets.
• Adaptive Peak Sizing: Dynamically adjusts peak sizes based on RNA abundance and specific contact patterns to reflect RNA-specific interaction preferences.
• Support for 'One-to-All' and 'All-to-All' Experiments: Analyzes both 'one-to-all' experiments focused on a single RNA and 'all-to-all' experiments capturing interactions among all RNAs in a sample.
• Robustness and Sparsity Handling: Produces robust peak calls that address the sparsity characteristic of genome-wide 'all-to-all' interaction data.

Scientific Applications:

• Elucidation of Non-Coding RNA Functions: Enables identification of genomic targets of chromatin-associated non-coding RNAs to study their roles in gene regulation.
• Insights into Chromatin Dynamics: Facilitates analysis of how chromatin heterogeneity influences RNA-DNA interaction patterns and regulatory architecture.

Methodology:

BaRDIC employs a tailored binomial model to identify peaks while integrating corrections for chromatin heterogeneity and distance-dependent decay and adapting peak sizes based on RNA-specific interaction patterns.