RCX

RCX converts and validates Cytoscape Exchange (CX) networks (JSON-based) to and from R native data structures to enable analysis, visualization, and exchange of biological networks.

Key Features:

• Integration with CX format: Create, manage, validate, and visualize biological networks in the Cytoscape Exchange (CX) format within R while preserving Cytoscape visual layouts.
• Conversion capabilities: Convert CX (JSON-based) networks into standard R data types and objects for downstream statistical and computational analysis.
• NDEx integration: Connect R with the Network Data Exchange (NDEx) to export, import, and synchronize network data for exchange and storage.
• Preservation of analytical results: Capture and retain results from network analyses within the CX format to maintain reproducible representations of analyses and visualizations.

Scientific Applications:

• Genomics and proteomics network analysis: Convert and prepare interaction networks for statistical analysis of genomic and proteomic data in R.
• Network visualization and interpretation: Preserve Cytoscape visual layouts and network structures to support interpretation of biological interactions and pathway representations.
• Collaborative network sharing: Exchange and store network datasets via NDEx to support collaborative analysis and reproducibility in systems biology research.

Methodology:

Automated conversion and validation between CX (JSON-based) and R native data structures, preservation of Cytoscape visual layouts, capture of analysis results in CX, and integration with NDEx.