HiCeekR: A Novel Shiny App for Hi-C Data Analysis

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• High-throughput Chromosome Conformation Capture (Hi-C) is crucial for studying genome-wide 3D chromatin organization.
• Existing Hi-C analysis tools often lack comprehensive pipelines, multi-omic integration, and user-friendly interfaces, primarily targeting expert users.

Purpose of the Study:

• To introduce HiCeekR, a novel R Graphical User Interface (GUI) designed for accessible and complete Hi-C data analysis.
• To provide a user-friendly platform that simplifies the complex process of analyzing 3D chromatin organization.

Main Methods:

• Development of HiCeekR, an R package utilizing Shiny libraries for an interactive GUI.
• Integration of established R/Bioconductor packages for comprehensive Hi-C data pre-processing, analysis, and visualization.
• Demonstration of HiCeekR's capabilities using a publicly available Hi-C dataset.

Main Results:

• HiCeekR offers an exhaustive analysis pipeline for Hi-C data, including identification of chromatin loops, topological associating domains, and A/B compartments.
• The GUI facilitates the integration and visualization of other omic data layers alongside Hi-C data.
• The tool guides users through the entire analysis process, reducing the need for command-line expertise.

Conclusions:

• HiCeekR significantly lowers the barrier to entry for researchers conducting Hi-C data analysis.
• The platform enhances the accessibility and efficiency of studying 3D genome architecture.
• HiCeekR empowers a broader range of researchers to perform advanced chromatin organization analyses.