TADCompare

TADCompare performs differential and temporal analysis of topologically associated domains (TADs) from Hi-C contact matrices to quantify and compare TAD boundary changes across conditions and timepoints.

Key Features:

• Differential TAD Analysis (TADCompare): Detects differences in TAD boundaries between two Hi-C datasets using a spectral clustering-derived eigenvector gap for loci-by-loci comparison.
• Time Course Analysis (TimeCompare): Tracks changes in chromatin architecture and TADs across time series or developmental stages.
• Consensus Boundary Identification (ConsensusTADs): Identifies consensus TAD boundaries across multiple Hi-C replicates to enhance reproducibility of boundary detection.
• Visualization (DiffPlot): Provides visual representations of differences between two contact matrices to aid interpretation of boundary changes.
• Colocalization and Gene Enrichment Analyses: Associates specific boundary changes with biological functions through colocalization and gene enrichment analyses.

Scientific Applications:

• Genome regulation studies: Quantifies chromatin architecture dynamics to investigate regulatory mechanisms mediated by TADs.
• Developmental and disease comparisons: Compares TAD boundary changes during development or between healthy and disease states to identify condition-specific alterations.
• Functional classification of boundary changes: Enables systematic classification of boundary alterations to reveal distinct biological functionalities linked to different change types.

Methodology:

TADCompare operates on Hi-C contact matrices and computes an eigenvector gap measure derived from spectral clustering for loci-by-loci TAD boundary comparison, and it performs colocalization and gene enrichment analyses to associate boundary changes with biological functions.