SIP (Significant Interaction Peak caller) is a tool to identify and analyze loops that appear as high intensity signal in Hi-C maps (.hic and .mcool files). This program is written in java and can be run on Linux, Windows, or MAC systems and includes either command line options or a graphical user interface.

Follow the links below to get started:

• Quick Start

If you use SIP or SIPMeta, please cite us.

Rowley MJ, Poulet A, Nichols MH, Bixler BJ, Sanborn AL, Brouhard EA, Hermetz K, Linsenbaum H, Csankovszki G, Lieberman Aiden E, Corces G. Analysis of Hi-C data using SIP effectively identifies loops in organisms from C. elegans to mammals. Genome Research 2020.