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Motivation: Computational analysis of chromosomal contact data is currently gaining popularity with the rapid advance in experimental techniques providing access to a growing body of data. An important problem in this area is the identification of long range contacts between distinct chromatin regions. Such loops were shown to exist at different scales, either mediating relatively short range interactions between enhancers and promoters or providing interactions between much larger, distant chromosome domains. A proper statistical analysis as well as availability to a wide research community are crucial in a tool for this task. Results: We present HiCEnterprise, a first freely available software tool for identification of long range chromatin contacts not only between small regions, but also between chromosomal domains. It implements four different statistical tests for identification of significant contacts for user defined regions or domains as well as necessary functions for input, output and visualization of chromosome contacts. Availability: The software and the corresponding documentation are available at: github. com/regulomics/HiCEnterprise.

Supplementary information: Supplemental data are available in the online version of the article and at the website regulomics. mimuw. edu. pl/wp/hicenterprise.