A custom aspect | Create the custom aspect in R | Update the aspect | Providing update methods | Update meta-data for the aspect | Witout a extension package | As extension package | Meta-data summary | Aspect references | Convenience methods | Validation of the aspect | Conversion to and from CX | Convert to CX | Conversion from CX/JSON | Session info

Introduction | Installation | Installation from Bioconductor | Installation from GitHub | Quick Start | Connect to a server | Find Networks | Simple network operations | RCX | Example Workflow | Aspects and Metadata | NDEx Network properties | API Compatibility with NDEx versions | Server REST API configuration

Introduction | The Cytoscape Exchange (CX) | The NDEx platform | Cytoscape | RCX - an adaption of the CX format | Installation | The basics | Read and write CX files | Explore the RCX object | Visualize the network | Validation | Get information about the networks | Conversion to R graph data models | igraph | Bioconductor graph (graphNEL) | Session info

The Cytoscape Exchange (CX) Format | Starting with nodes and edges | Adding attributes to the network | Node Attributes | Network Attributes | Put the nodes into position | Create visual layout | Visual properties of the network | Visual properties of nodes | Visual properties of edges | Create a visual property aspect | Table column | Visualize the final network | Meta-data | Create RCX at once | Save the network | Session info

CX data structure | Aspect dependencies | Data types | NDEx conventions | Handling of Identifiers | Citations | Meta aspects | metaData | status | Core aspects | nodes | edges | nodeAttributes | edgeAttributes | networkAttributes | cartesianLayout | Cytoscape aspects | cyGroups | CyVisualProperties | CyVisualProperties (CX) | CyVisualProperties (RCX) | CyVisualProperty | CyVisualPropertyProperties | CyVisualPropertyDependencies | CyVisualPropertyMappings | cyHiddenAttributes | cyNetworkRelations | cySubNetworks | cyTableColum | Deprecated aspects | Session info