LoopRig is an R package that aims to standardize complexcoordinate-based workflows utilizing chromatin loop and genomic elementdata.
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 BEDPEfiles is used as input for theLoopsToRanges() andElementsToRanges() functions, which create S3 containersfor S4GRangesList andGRanges objects respectively.These containers are of classLoopRanges andElementRanges, and can be analyzed using the chromatin loopmanipulation 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 availablehere