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# Mariner: Explore the Hi-Cs <img src="man/figures/mariner.png" id="mariner_logo" align="right" width="150px" style="padding-left:20px; background-color:white"/> <!-- badges: start --> ![GitHub R package version]( [![Codecov test coverage](]( [![DOI](]( <!-- badges: end --> ## 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. <div class = "row"> <div class = "col-md-4"> <b>One ecosystem</b><br> <code>mariner</code> extends common Bioconductor classes, leveraging the thousands of existing tools for analyzing and visualizing genomic data. </div> <div class = "col-md-4"> <b>Modular design</b><br> <code>mariner's</code> functions can be combined and chained in various ways to produce custom workflows. </div> <div class = "col-md-4"> <b>Fast and efficient</b><br> <code>mariner</code> leverages HDF5 to store large results and uses block processing to minimize hardware requirements. </div> </div> ## Key features <div class="row"> <div class="col-md-6" style="margin-bottom:20px; max-width:500px"> <b>Manipulating Paired Ranges</b><br> <i>Convert, bin, and shift paired genomic ranges</i> <img src="man/figures/binningFigure2.png" style="padding-top:20px;"></img> </div> <div class="col-md-6" style="margin-bottom:20px; max-width:500px"> <b>Clustering & Merging Interactions</b><br> <i>Group nearby interactions and select one as representative</i> <img src="man/figures/mergingFigure.png" style="padding-top:20px;"></img> </div> </div> <div class="row"> <div class="col-md-6" style="margin-bottom:20px; max-width:500px"> <b>Extracting & Aggregating Interactions</b><br> <i>Pull Hi-C pixels or matrices, then aggregate by files or interactions</i> <img src="man/figures/aggregateFigure.png" style="padding-top:20px;"></img> </div> <div class="col-md-6" style="margin-bottom:20px; max-width:500px"> <b>Calculating Loop Enrichment</b><br> <i>Determine loop enrichment to local background with selection functions to flexibility select foreground and background.</i> <img src="man/figures/enrichmentFigure.png" style="padding-top:20px;"></img> </div> </div> ## Installation This package can be installed through Bioconductor: ```{r} if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("mariner") ``` Or the development version can be installed via GitHub: ```{r} if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes") remotes::install_github("EricSDavis/mariner") ```