diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data

Online resources and supplemental information

Authors

Caleb Lareau and Martin Aryee

Links

• Code repository hosted on GitHub.
• Detailed HTML Vignette, which contains a reproducible walk-through the core functionality of diffloop. Cloning and analyzing the data in the repository linked above enables users to similarly follow the analysis structure of the vignette.
• Writeup comparing variable contains a .pdf writeup of assessing differential looping associations under different model specifications. In particular, we assess specifying negative binomial regression models compared to using limma/voom as well as examine performing variable differential loop association as a function of binned loop distance.

About

This repository contains more detailed use cases and analyses associated with the diffloop workflow. Figure 1 was created using the R/Shiny interface DNAlandscapeR.

Important information

• Install git large file storage before cloning repository to access full data (~ 2 GB total).

• Link to ChIA-PET Pre-processing software: mango

• A recent version of diffloop is required to run the code in this repository. We'd recommend installing from Bioconductor to ensure a recent, stable version--

  source("https://bioconductor.org/biocLite.R")
  biocLite("diffloop")

• An older vignette showcasing some additional functionality and analysis not highlighted in this repository can be found here.