Mariner: explore the Hi-Cs

Abstract Motivation 3D chromatin structure plays an important role in regulating gene expression and alterations to this structure can result in developmental abnormalities and disease. While genomic approaches like Hi-C and Micro-C can provide valuable insights in 3D chromatin architecture, the res...

Full description

Saved in:
Bibliographic Details
Published in:Bioinformatics (Oxford, England) England), 2024-06, Vol.40 (6)
Main Authors: Davis, Eric S, Parker, Sarah M, Kramer, Nicole E, Flores, J P, Kiran, Manjari, Phanstiel, Douglas H
Format: Article
Language:English
Subjects:
Abnormalities
Applications Note
Availability
Chromatin
Chromatin - chemistry
Chromatin - metabolism
Computational Biology - methods
Extreme values
Gene expression
Genomics - methods
Humans
HyperText Markup Language
Software
Workflow
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Abstract Motivation 3D chromatin structure plays an important role in regulating gene expression and alterations to this structure can result in developmental abnormalities and disease. While genomic approaches like Hi-C and Micro-C can provide valuable insights in 3D chromatin architecture, the resulting datasets are extremely large and difficult to manipulate. Results Here, we present mariner, a rapid and memory efficient tool to extract, aggregate, and plot data from Hi-C matrices within the R/Bioconductor environment. Mariner simplifies the process of querying and extracting contacts from multiple Hi-C files using a parallel and block-processing approach. Modular functions allow complete workflow customization for advanced users, yet all-in-one functions are available for running the most common types of analyses. Finally, tight integration with existing Bioconductor infrastructure enables complete analysis and visualization of Hi-C data in R. Availability and implementation Available on GitHub at https://github.com/EricSDavis/mariner and on Bioconductor at https://www.bioconductor.org/packages/release/bioc/html/mariner.html.
ISSN:1367-4811
1367-4803
1367-4811
DOI:10.1093/bioinformatics/btae352