DNA Rchitect: an R based visualizer for network analysis of chromatin interaction data

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Genomic data visualization often relies on commercial or hosted browsers.
• Flexible visualization of chromatin interaction data is crucial for understanding gene expression.
• There is a need for open-source tools for visualizing HiC and chromatin conformation data.

Purpose of the Study:

• Introduce DNA Rchitect, a novel open-source application for visualizing HiC and chromatin conformation data.
• Provide a tool for interactive network analyses alongside genomic feature visualization.
• Facilitate insights into gene expression through advanced data visualization.

Main Methods:

• Developed DNA Rchitect as a web application and open-source software.
• Utilized R for primary development.
• Enabled users to upload pre-filtered HiC data in bedpe format.

Main Results:

• DNA Rchitect visualizes HiC and chromatin conformation contacts at high (Kb) and low (Mb) resolutions.
• The tool supports visualization of various genomic data types and performs network analyses.
• Users can download results for further analysis in network programs like Cytoscape.

Conclusions:

• DNA Rchitect offers a flexible and open-source solution for HiC and chromatin conformation data visualization.
• The application enhances the understanding of genomic interactions and gene expression.
• Freely available web application and open-source code promote accessibility and further development.