diffloop

An R package for identifying differential features from chromatin capture confirmation experiments.

Quick Start

Raw FASTQ read files can be preprocessed with the mango (https://github.com/dphansti/mango) software, an R package that relies on bowtie, bedtools, and MACS2 to align reads, call anchor peaks, and summarize PETs per sample in the ChIA-PET experiment.

Sample analysis with diffloop

Check out the vignette for a working example on quality control, visualization, association, and annotation.

Interactive visualization

Check out DNAlandscapeR for an R/Shiny environment to visualize topology data interactively.

Contact

Caleb Lareau is the primary maintainer/developer of diffloop.