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Updated: Jun 15, 2026

Capturing Chromosome Conformation Across Length Scales

Capturing Chromosome Conformation Across Length Scales

Published on: January 20, 2023

HiCmapTools: a tool to access HiC contact maps.

Jia-Ming Chang¹, Yi-Fu Weng², Wei-Ting Chang²

¹Department of Computer Science, National Chengchi University, 11605, Taipei City, Taiwan. chang.jiaming@gmail.com.

BMC Bioinformatics

|February 11, 2022

Summary

This summary is machine-generated.

HiCmapTools is a new software for analyzing Hi-C data, enabling biologists to efficiently query and extract biological insights from contact maps. It supports multiple analysis modes for investigating genomic interactions.

Keywords:

3D genome Hi-C Juicer Topologically Associating Domains (TADs)hicpipe

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Last Updated: Jun 15, 2026

Capturing Chromosome Conformation Across Length Scales

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Published on: January 20, 2023

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Published on: October 14, 2022

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

High-throughput chromosome conformation capture (Hi-C) technology generates vast amounts of sequencing data.
Existing tools effectively create Hi-C contact maps but lack functionalities for querying and extracting biological information.
A need exists for specialized tools to analyze and interpret Hi-C datasets for biological insights.

Purpose of the Study:

To develop and present HiCmapTools, a novel software solution for efficient Hi-C map analysis.
To provide biologists with a tool for querying Hi-C contact maps to extract meaningful biological information.
To validate the utility of HiCmapTools on key biological questions such as TAD loops and intra-TAD density.

Main Methods:

Development of HiCmapTools, a comprehensive software package implemented in C++ and R.
Integration of multi-query modes and diverse analysis tools within the software.
Validation of the tool's performance using real biological datasets addressing specific genomic architecture questions.

Main Results:

HiCmapTools enables efficient calculation and analysis of Hi-C maps.
The software offers multi-query capabilities and various analysis functions.
Successful validation on biological questions including TAD loop identification and TAD intra-density analysis.

Conclusions:

HiCmapTools provides biologists with seven access options for quantifying contact frequencies at specific genomic sites.
The tool facilitates the extraction of biological information from Hi-C datasets.
HiCmapTools is freely available with comprehensive documentation for widespread adoption and use.