1. Mariner: explore the Hi-Cs.
- Author
-
Davis, Eric S, Parker, Sarah M, Kramer, Nicole E, Flores, J P, Kiran, Manjari, and Phanstiel, Douglas H
- 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. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF