LoopRig is an R package that aims to standardize complex coordinate-based workflows utilizing chromatin loop and genomic element data.
LoopRig can be installed directly from GitHub:
# install.packages("devtools")
devtools::install_github("hsmaan/LoopRig", build_vignettes = TRUE)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