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Related Experiment Video

Updated: Jun 25, 2025

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

Mariner: explore the Hi-Cs.

Eric S Davis^1,2, Sarah M Parker¹, Nicole E Kramer¹

¹Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States.

Bioinformatics (Oxford, England)

|May 30, 2024

Summary

This summary is machine-generated.

Mariner is a new R/Bioconductor tool that efficiently processes large Hi-C datasets for 3D chromatin structure analysis. It simplifies extracting, aggregating, and plotting genomic contact data, aiding research into gene expression and disease.

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Capturing Chromosome Conformation Across Length Scales

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Published on: January 20, 2023

Area of Science:

Genomics
Computational Biology
Molecular Biology

Background:

3D chromatin structure is crucial for gene regulation.
Aberrations in chromatin structure are linked to developmental disorders and diseases.
High-throughput chromosome conformation capture (Hi-C) techniques generate large, complex datasets.

Purpose of the Study:

To introduce mariner, a novel software tool for analyzing Hi-C data.
To provide a rapid and memory-efficient solution for processing large Hi-C matrices.
To facilitate the extraction, aggregation, and visualization of 3D chromatin contact data.

Main Methods:

Mariner utilizes a parallel and block-processing approach for efficient data handling.
The tool offers modular functions for customized analysis workflows.
Integrated functions enable common Hi-C analyses within the R/Bioconductor environment.

Main Results:

Mariner significantly speeds up the extraction and aggregation of Hi-C contact data.
The software efficiently handles large Hi-C matrices, reducing computational burden.
Seamless integration with Bioconductor allows for comprehensive data analysis and visualization.

Conclusions:

Mariner provides a powerful and user-friendly solution for 3D chromatin structure analysis.
The tool enhances the accessibility and efficiency of Hi-C data interpretation.
Mariner supports advanced customization while offering straightforward options for standard analyses.