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

R N Ramirez1, K Bedirian1,2, S M Gray1

  • 1Department of Immunology, Harvard Medical School, Boston, MA, 02115, USA.

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Summary
This summary is machine-generated.

DNA Rchitect is a new open-source tool for visualizing HiC and chromatin conformation data. This application provides interactive network analyses and visualization of genomic features for gene expression insights.

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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.