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| rTRM-package | Identification transcription regulatory modules (TRMs) |
| 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 |
| removeVertices | Remove nodes from a graph and returns the largest component |
| rTRM | Identification transcription regulatory modules (TRMs) |
| writeTRMreport | Export a table with TRM nodes and associated information. |