SpectralTAD

"SpectralTAD" is an R package that introduces a novel sliding window-based spectral clustering framework for identifying topologically associated domains (TADs) in Hi-C data. This method utilizes gaps between consecutive eigenvectors for TAD boundary identification, offering advantages such as automatic parameter selection, robustness to data biases, sequencing depth, resolution, and sparsity. SpectralTAD outperforms existing TAD callers in both simulated and experimental scenarios. The tool facilitates the detection of hierarchical, biologically relevant TADs and highlights distinctions in TAD boundaries, providing insights into the dynamic roles of these structures in genome regulation.