Introduction | Publication | Installation | Installation via Github | Load the package | Test the package | Create new mully graph | Add Layers | Add/print Nodes | Add/print/remove Edges | Merge two graphs | Visualization | Available Functions | addEdge | addLayer | addNode | exportCSV | getEdgeAttributes | getIDEdge | getIDNode | getLayer | getLayersCount | getNode | getNodeAttributes | importEdgesCSV | importGraphCSV | importLayersCSV | importNodesCSV | is.mully | isLayer | merge | mully | plot,mully | plot3d | print,mully | removeEdge | removeLayer | removeNode

Introduction | Publication | Installation | Installation via Github | Load the package | Test the package | Create new mully graph | Add Layers | Add/print Nodes | Add/print/remove Edges | Merge two graphs | Visualization | Available Functions | addEdge | addLayer | addNode | exportCSV | getEdgeAttributes | getIDEdge | getIDNode | getLayer | getLayersCount | getNode | getNodeAttributes | importEdgesCSV | importGraphCSV | importLayersCSV | importNodesCSV | is.mully | isLayer | merge | mully | plot,mully | plot3d | print,mully | removeEdge | removeLayer | removeNode

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

Introduction | Installation Instructions | Getting Started | Downloading BioPAX Data | Parsing BioPAX Data | Internal Data Model | Accessing the Data | Visualization | Modifying BioPAX | Writing out in BioPAX Format | Example: Parsing Reactome Biopax Level 3 | Session Information