diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data
Online resources and supplemental information
Caleb Lareau and Martin Aryee
- 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
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.
This repository contains more detailed use cases and analyses associated with the
Figure 1 was created using the R/Shiny interface DNAlandscapeR.
- 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–
- An older vignette showcasing some additional functionality and analysis not highlighted in this
repository can be found here.