Integration and Analysis of Chromatin Loop Data

Common coordinate-based workflows involving processed chromatin loop and genomic element data are considered and packaged into appropriate customizable functions. Includes methods for linking element sets via chromatin loops and creating consensus loop datasets.

LoopRig

Overview

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

Installation

LoopRig can be installed directly from GitHub:

# 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:

browseVignettes("LoopRig")
vignette("LoopRig-Tutorial")

Complete package documentation available here

License

GNU General Public License 3.0