covNorm

covNorm normalizes Hi-C and capture Hi-C data to correct DNA fragment coverage biases, remove genomic distance-dependent background, and identify significant chromatin interactions for analysis of chromatin architecture.

Key Features:

• Implicit normalization (covNorm): Implements the covNorm implicit normalization technique as an R package for Hi-C and capture Hi-C protocols.
• Negative binomial normalization: Applies a negative binomial model to normalize DNA fragment coverages.
• Genomic-distance background removal: Removes genomic distance-dependent background signal from contact data.
• Interaction detection: Identifies significant chromatin interactions after normalization and background removal.
• Protocol extendibility: Can be adapted to derivative Hi-C protocols.

Scientific Applications:

• Reproducibility assessment: Produces improved or comparable reproducibility metrics such as HiC-spector scores and compartment A/B profile correlations relative to baseline methods.
• Long-range contact detection: Enables detection of significant long-range chromatin contacts for studies of higher-order chromatin structure.

Methodology:

Sequential processing using a negative binomial model-based normalization of DNA fragment coverages, removal of genomic distance-dependent background, and identification of significant chromatin interactions.