| adjM2gml | Create GML file from readAmigoDot output. |
| AmigoDot | AmigoDot constructor and accessors |
| AmigoDot-class | Class "AmigoDot" |
| AmigoDot.to.Cyto | Opening the AmigoDot graph in Cytoscape through RCytoscape. |
| AmigoDot.to.graphAM | Converts an AmigoDot S4 object to a graphAM object. |
| AmigoDot.to.graphNEL | Converts an AmigoDot S4 object to a graphNEL object. |
| c5.go.mapping | MSigDB C5 GO term to GO ID mapping |
| exportCytoGML | Writes out an igraph graph to a Cytoscape readable GML file. |
| getAmigoTree | Getting the DAG GO tree for a set of GO ID's. |
| igraph-class | Class '"igraph"' |
| RamiGO-package | AmiGO visualize R interface |
| readAmigoDot | Parser for the GraphViz DOT format. |
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