RCX

RCX implements the Cytoscape Exchange (CX) format in R to create, handle, validate, visualize, and convert biological networks to standard data types and objects.

Key Features:

• CX Format Support: Provides full implementation of the Cytoscape Exchange (CX) format for network data representation in R.
• Network Conversion: Converts networks to and from iGraph and graphNEL objects.
• Network Validation: Validates network structures in CX format.
• Network Visualization: Supports visualization of CX format networks.
• NDEx Platform Compatibility: Enables interoperability with the NDEx platform, an online commons for biological networks.
• Cytoscape Integration: Supports exchange with the Cytoscape network visualization software.

Scientific Applications:

• Biological Network Analysis: Facilitates analysis of biological networks stored in the NDEx platform commons.
• Network Data Exchange: Enables standardized sharing of biological network data between R, Cytoscape, and NDEx.
• Cross-Platform Network Workflow: Supports integration of network analysis workflows across iGraph, graphNEL, Cytoscape, and NDEx environments.

Methodology:

The package implements R data structures and methods for parsing, constructing, and manipulating CX format networks, with conversion functions mapping CX network elements to iGraph and graphNEL object representations.