---
title: "diffloopdata: An example ChIA-PET dataset for the diffloop package"
author: "Caleb Lareau and Martin Aryee"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{diffloopdata}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

The `diffloopdata` package contains an example dataset for use with the
diffloop package. 

It contains chromosome 1 data from 6 ChIA-PET samples.$^{1,2}$ The raw FASTQ
read files were preprocessed with the `dnaloop`
(https://github.com/aryeelab/dnaloop) package. 


$^1$Hnisz, Denes, et al. "Activation of proto-oncogenes by disruption of
chromosome neighborhoods." Science (2016): aad9024. <br><br>
$^2$Ji, Xiong, et al. "3D Chromosome Regulatory Landscape of Human Pluripotent
Cells." Cell stem cell (2015).

