PanChIP is a pan-ChIP-seq protein colocalization analysis algorithm created in python.

Sanidas I, Lee H, Rumbe PH, Boulay G, Morris R, Golczer G, Stanzione M, Hajizadeh S, Zhong J, Ryan MB, Corcoran RB, Drapkin BJ, Rivera MN, Dyson NJ†, & Lawrence MS†. Chromatin-bound RB targets promoters, enhancers, and CTCF-bound loci and is redistributed by cell-cycle progression. Molecular Cell 82.18, 3333–3349. (Article, PDF)

Lee H†, Sanidas I, Dyson NJ, & Lawrence MS†. Chromatin-bound protein colocalization analysis using bedGraph2Cluster and PanChIP. STAR Protocols 4.1, 101991. (Article, PDF)


HiCShuffle is a FASTQ shuffling tool for sanity check in Hi-C differential contact analysis

Lee H†, Blumberg B, Lawrence MS, & Shioda T†. Revisiting the Use of Structural Similarity Index in Hi-C. Nature Genetics 55, 2049–2052 (Article, PDF, bioRxiv)