| Function | Description |
| acc-methods | Methods for Accessibility Lists |
| addEdge | addEdge |
| addNode | addNode |
| adj-methods | Methods for finding the adjacency list for selected nodes. |
| aM2bpG | Coercions between matrix and graph representations |
| apopGraph | KEGG apoptosis pathway graph |
| asGraphProperty | Generic for converting input to graph property list |
| aveNumEdges | Calculate the average number of edges in a graph |
| biocRepos | A graph representing the Bioconductor package repository |
| boundary | Returns the Boundary between a Graph and a SubGraph |
| buildRepDepGraph | Functionality to manage repository dependency graphs |
| calcProb | Calculate the hypergeometric probability of the subgraph's number of edges. |
| calcSumProb | Calculate the probability that a subgraph has an unusual number of edges. |
| clearNode | clearNode |
| clusterGraph-class | Class "clusterGraph" |
| clusteringCoefficient | Clustering coefficient of a graph |
| combineNodes | combineNodes |
| DFS | Depth First Search |
| distGraph-class | Class "distGraph" |
| duplicatedEdges | duplicatedEdges |
| edgeMatrix | Compute an Edge Matrix or weight vector for a Graph |
| edgeWeights | Retrieve the edge weights for specified indices. |
| fromGXL-methods | Methods for GXL manipulations in package graph |
| ftM2int | Standard labeling of edges with integers |
| gEdge-class | Class "gEdge" |
| generalGraph-class | Class "generalGraph" ~~~ |
| gNode-class | Class "gNode" |
| graph2SparseM | Coercion methods between graphs and sparse matrices |
| graph-class | Class "graph" |
| graphExamples | A List Of Example Graphs |
| graphH-class | Class "graphH" |
| graphID-class | Unique Graph Identifications |
| graphNEL-class | Class "graphNEL" |
| hashtable | Create a hashtable |
| hashtable-class | Class "hashtable" |
| inEdges | inEdges |
| integrinMediatedCellAdhesion | KEGG Integrin Mediated Cell Adhesion graph |
| listEdges | List the Edges of a Graph |
| mostEdges | Find the node in a graph with the greatest number of edges |
| numEdges | Calculate the number of edges in a graph |
| numNoEdges | Calculate the number of nodes that have an edge list of NULL |
| propertyHolder-class | Class "propertyHolder" |
| randomEGraph | Random Edge Graph |
| randomGraph | Random Graph |
| randomNodeGraph | Generate a Graph with specified degree distribution. |
| removeEdge | removeEdge |
| removeNode | removeNode |
| simpleEdge-class | Class "simpleEdge". |
| subGraph | Create a Subgraph |
| ugraph | Underlying Graph |
| validGraph | Test whether graph object is valid |
| write.tlp | Write a graph object in a file in the Tulip format |