Bioconductor Code: mariner (original) (raw)
# Mariner: Explore the Hi-Cs 
 [\](https://codecov.io/gh/EricSDavis/mariner?branch=dev) [\](https://zenodo.org/badge/latestdoi/475953890) ## Why mariner? Disruption or aberrant formation of chromatin interactions can result in developmental abnormalities and disease. Therefore, deriving biological insights from 3D chromatin structure experiments, such as Hi-C or Micro-C, is essential for understanding and correcting human disease. `mariner` is an R/Bioconductor package for exploring Hi-C data. It enables users to flexibly manipulate, extract, and aggregate chromatin interaction data quickly and efficiently.
](https://codecov.io/gh/EricSDavis/mariner/branch/dev/graph/badge.svg)\](https://codecov.io/gh/EricSDavis/mariner?branch=dev)){kind=link}
](https://zenodo.org/badge/475953890.svg)\](https://zenodo.org/badge/latestdoi/475953890)){kind=link}
mariner extends common Bioconductor classes, leveraging the thousands of existing tools for analyzing and visualizing genomic data. mariner's functions can be combined and chained in various ways to produce custom workflows. mariner leverages HDF5 to store large results and uses block processing to minimize hardware requirements. Convert, bin, and shift paired genomic ranges
Group nearby interactions and select one as representative
Pull Hi-C pixels or matrices, then aggregate by files or interactions
Determine loop enrichment to local background with selection functions to flexibility select foreground and background.
