IceDP: identifying inter-chromatin engagement via density peaks clustering algorithm.

ABSTRACT: Chromatin topological structure is critical for gene regulation. Hi-C based experiments have significantly advanced our understanding chromatin organization. Numerous computational tools have been developed to identify various structural levels of chromatin, ranging from compartments to loops. However, there remains a lack of specialized tools for identifying non-homologous inter-chromatin contacts (NHCCs), which play important roles in chromosome territories. In this study, we present iceDP, a tool that leverages the Density Peaks clustering algorithm to identify local high-density regions within inter-chromatin. These regions undergo two subsequent filtering steps to eliminate obvious false positives. When applied to three Hi-C datasets, iceDP accurately identified known NHCCs, including

SUBMITTER: Chen R 

PROVIDER: S-EPMC12777978 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature