HiC1Dmetrics

HiC1Dmetrics extracts and analyzes one-dimensional (1D) metrics from Hi-C contact matrices to quantify and compare chromatin structural features and integrate them with epigenomic tracks for chromatin-state annotation.

Key Features:

• 1D metric extraction: Extracts one-dimensional metrics from two-dimensional Hi-C contact matrices to represent chromosome structure along the genome.
• Evaluation of existing metrics: Reviews and assesses existing 1D metrics for individual Hi-C samples and two-sample comparisons, identifying suitable scenarios for their application.
• Novel 1D metrics: Implements newly introduced 1D metrics that capture structural features of chromosomes not accessible through traditional methods.
• Multi-sample comparison and visualization: Provides metrics suitable for reproducible and robust comparison and visualization across multiple Hi-C samples.
• Integration with epigenome tracks: Aligns 1D Hi-C metrics with epigenomic tracks to facilitate annotation of chromatin states.

Scientific Applications:

• Chromatin structure quantification: Quantifies local and regional chromatin structural features from Hi-C data using 1D summaries.
• Pairwise sample comparison: Compares structural differences between two Hi-C samples using evaluated 1D metrics.
• Multi-sample analysis: Enables comparison and visualization of structural patterns across multiple Hi-C datasets for reproducibility assessments.
• Chromatin-state annotation: Integrates 1D Hi-C metrics with epigenomic tracks to aid annotation of chromatin states.

Methodology:

Computational steps explicitly include extracting 1D metrics from two-dimensional Hi-C contact matrices, evaluating existing 1D metrics for single-sample and two-sample comparisons, computing novel 1D metrics, and integrating 1D profiles with epigenomic tracks.