Loopsim: Enrichment Analysis of Chromosome Conformation Capture with Fast Empirical Distribution Simulation
Listed in
This article is not in any list yet, why not save it to one of your lists.Abstract
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.