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. 2024 Jun 3;40(6):btae352.
doi: 10.1093/bioinformatics/btae352.

Mariner: explore the Hi-Cs

Eric S Davis  1   2 , Sarah M Parker  1 , Nicole E Kramer  1 , J P Flores  1 , Manjari Kiran  3 , Douglas H Phanstiel  1   2   4   5   6
Affiliations

Mariner: explore the Hi-Cs

Eric S Davis et al. Bioinformatics. .

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.

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Conflict of interest statement

None declared.

References

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