diffloop is a tool for identification and analysis of differential DNA looping data from assays like HiChIP and ChIA-PET. diffloop is distributed as a Bioconductor package to facilitate the

Availability: diffloop Bioconductor Package
Vignettes: diffloop vignettes page

Lareau, C. A., & Aryee, M. J. (2017). diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data. Bioinformatics. Accepted.


Genome-wide Unbiased Identifications of DSBs Evaluated by Sequencing (GUIDE-seq) is a method developed in the Joung lab to identify the off-target sites of CRISPR-Cas RNA-guided Nucleases. The guideseq python package implements our data preprocessing and analysis pipeline for GUIDE-Seq data.

Availability: guideseq source page

Tsai, S. Q., Topkar, V. V., Joung, J. K., & Aryee, M. J. (2016). Open-source guideseq software for analysis of GUIDE-seq data. Nature biotechnology, 34(5), 483-483.


hichipper is a preprocessing tool for HiChIP data that calls DNA loops from aligned sequencing data. hichipper corrects for biases associated with restriction enzyme digestion and enriches for long-range loops mediated by a factor of interest.

Availability: hichipper landing page
Documentation: hichipper Documentation

Lareau, C. A., & Aryee, M. J. (2017). hichipper: A preprocessing pipeline for assessing library quality and DNA loops from HiChIP data. Nature Methods. Accepted.