DNA Rchitect

DNA Rchitect visualizes and analyzes chromatin interaction data to reveal spatial genome organization from HiC and other chromatin conformation datasets.

Key Features:

• Data Visualization: Visualizes HiC and chromatin conformation data at kilobase and megabase resolutions using 2D-arc representations of chromatin interactions.
• Network Analysis: Performs network analysis on interaction data to explore complex interaction networks relevant to gene expression regulation and chromatin architecture.
• Multi-Format Support: Supports bed, bedgraph, and bedpe file formats for input and processing of genomic interaction and signal data.
• Integration with External Tools: Exports interaction and network results for downstream analysis in network-focused programs such as Cytoscape.

Scientific Applications:

• Chromatin Architecture Studies: Investigating three-dimensional genome organization and chromatin topology using HiC and related datasets.
• Gene Regulation Analysis: Assessing spatial relationships between genomic elements that influence gene expression regulation.
• Multi-Resolution Interaction Analysis: Analyzing large-scale interaction datasets across kilobase to megabase resolutions to capture both fine- and broad-scale contacts.

Methodology:

Implemented in R using Shiny, employing R wrappers for HTML, CSS, and JavaScript, with R code executed in a reactive web environment powered by NodeJS.