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