README.Rmd

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output: github_document
---

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```{r, include = FALSE}
knitr::opts_chunk$set(
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  fig.path = "man/figures/README-",
  out.width = "100%",
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```

# LoopRig <img src="man/figures/looprig_logo.png" height="180px" align="right"/>

[![CRAN status](https://www.r-pkg.org/badges/version/LoopRig)](https://cran.r-project.org/package=LoopRig)
[![Build Status](https://travis-ci.com/hsmaan/LoopRig.svg?token=jBqxwnZzU1qwLZyzpxME&branch=master)](https://travis-ci.com/hsmaan/LoopRig)
[![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/hsmaan/LoopRig?branch=master&svg=true)](https://ci.appveyor.com/project/hsmaan/LoopRig)
[![codecov](https://codecov.io/gh/hsmaan/LoopRig/branch/master/graph/badge.svg)](https://codecov.io/gh/hsmaan/LoopRig)

## Overview

LoopRig is an R package that aims to standardize complex coordinate-based workflows utilizing chromatin loop and genomic element data. 

## Installation

LoopRig is available on CRAN and can be installed using:
```r
install.packages("LoopRig")
```

Alternatively, LoopRig can also be installed directly from GitHub:
``` r
# install.packages("devtools")
devtools::install_github("hsmaan/LoopRig", build_vignettes = TRUE)
```
## Usage

Element data from BED4..n files and chromatin loop data from BEDPE files is used as input for the `LoopsToRanges()` and `ElementsToRanges()` functions, which create S3 containers for S4 *GRangesList* and *GRanges* objects respectively. These containers are of class *LoopRanges* and *ElementRanges*, and can be analyzed using the chromatin loop manipulation and element linkage functions available in LoopRig. 

An in-depth tutorial is available in the package vignettes:
```r
browseVignettes("LoopRig")
vignette("LoopRig-Tutorial")
```
Complete package documentation available [here](https://hsmaan.github.io/LoopRig/)

## License 

[GNU General Public License 3.0](https://github.com/hsmaan/LoopRig/blob/master/LICENSE)