A comprehensive review and benchmark of differential analysis tools for Hi-C data.

ABSTRACT:

Motivation

The 3D organization of the genome plays a crucial role in various biological processes. Hi-C technology is widely used to investigate chromosome structures by quantifying 3D proximity between genomic regions. While numerous computational tools exist for detecting differences in Hi-C data between conditions, a comprehensive review and benchmark comparing their effectiveness is lacking.

Results

This study offers a comprehensive review and benchmark of 10 generic tools for differential analysis of Hi-C matrices at the interaction count level. The benchmark assesses the statistical methods, usability, and performance (in terms of precision and power) of these tools, using both real and simulated Hi-C data. Results reveal a striking variability in performance among the

SUBMITTER: Jorge E 

PROVIDER: S-EPMC11879411 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature