Loopsim: Enrichment Analysis of Chromosome Conformation Capture with Fast Empirical Distribution Simulation

Summary Gene regulation is intricately influenced by the three-dimensional organization of the genome. In particular, chromatin can exist in loop structures that enable long-range regulatory interactions. By utilizing chromosome conformation capture techniques such as Hi-C, valuable information regarding the organization of these loop structures in 3D space can be obtained. While functional/feature enrichment has become a standard downstream analysis for different genomic data to provide biological context, tools that developed specifically for high throughput assays capturing chromosome conformation are relatively limited. Here, we present Loopsim, a command-line application that performs enrichment analysis on Hi-C loop profiles against user-defined regions. Loopsim efficiently simulates a background distribution using a distinctive sampling approach that considers loop size, intervals, loop-loop distances, and structure; it then computes loop-level statistics based on the empirical null distribution. Availability Loopsim is a Python package available via PyPI ( https://pypi.org/project/loopsim ) and the source code is available on GitHub ( https://github.com/CutaneousBioinf/Loopsim ) under the MIT license.