Sample Analysis for diffloop paper
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README.md
diffloop_supplement_23September.docx

README.md



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.