annotateFreq            Annotate a graph with frequency of nodes/edges
                        in other graphs.
annotateModule          Annotate a network module with information
annotateTRM             Annotate a network object with information
                        about clusters.
biogrid_hs              Network dataset of class 'igraph'
biogrid_mm              Network dataset of class 'igraph'
findTRM                 Indentifies a TRM associated with a target node
                        and one or more query nodes.
getAnnotations          Obtain the 'pwm' table fromt the database,
                        containing PWM's annotations.
getBiogridData          Downloads network data from BioGRID in TAB2
                        format.
getConcentricList       Returns a list with nodes membership to be used
                        in a graph with a concentric layout
getLargestComp          Gets the largest connected component
getMaps                 Obtain the mapping between PWM and Entrez Gene
                        identifiers.
getMatrices             Obtain a list of PWMs.
getMotifsFromEntrezgene
                        Retrieve PWMs associated with genes provided as
                        entrezgene identifiers.
getMotifsFromSymbol     Retrieve PWMs associated with genes provided as
                        symbol.
getOrthologFromMatrix   Obtain gene identifiers for a target organism
                        associated with a list of PWMs.
getOrthologs            Obtain the mapping to Entrez Gene identifiers
                        in the given organism.
getOrthologsFromBiomart
                        Returns ortholog genes for a target organism
getSequencesFromGenome
                        Retrieves a set of sequences from a BSgenome
                        object and optionally appends a label to each
                        sequence id.
getSimilarityMatrix     Compute similarity matrix of list of graphs.
getTFclass              Return the ontology in the TFclass database
                        associated with an entrezgene identifier
getTFclassFromEntrezgene
                        Applies getTFclass sequentially to a vector of
                        entrezgene identifiers.
getTFterms              Get terms associated with a specified TFclass
                        subset.
initBiomart             Initializes mart objects to identify ortholog
                        genes
layout.arc              Layouts a graph using arcs.
layout.concentric       Generates a concentric layout for graphs
plotDegree              Plot degree distribution for network nodes
plotGraph               Plot an graph in igraph format.
plotTRM                 Plot an annotated TRM.
plotTRMlegend           Plot the legend of a TRM with information about
                        the cluster families.
processBiogrid          Process a data.frame with BioGRID data into a
                        network for a target organism
rTRM-package            Identification transcription regulatory modules
                        (TRMs)
removeVertices          Remove nodes from a graph and returns the
                        largest component
writeTRMreport          Export a table with TRM nodes and associated
                        information.
