# 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"/>
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## 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.
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<b>One ecosystem</b><br>
<code>mariner</code> extends common Bioconductor classes, leveraging the thousands of
existing tools for analyzing and visualizing genomic data.
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<b>Modular design</b><br>
<code>mariner's</code> functions can be combined and chained in various ways to produce
custom workflows.
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<b>Fast and efficient</b><br>
<code>mariner</code> leverages HDF5 to store large results and uses block processing
to minimize hardware requirements.
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## Key features
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<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>
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<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>
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<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>
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<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>
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## 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")
```
