assignEdgeWeights | Assigning weights to network edges |
biopax2igraph | Processes BioPAX objects into igraph objects |
colorVertexByAttr | Computes colors for vertices according to their attributes. |
ex_biopax | Biopax example data |
ex_kgml_sig | Singaling network from KGML example |
ex_microarray | An microarray data example. |
ex_sbml | Metabolic network from SBML example |
extractPathNetwork | Creates a subnetwork from a ranked path list |
getAttr | Get / Set vertex attribute names and coverage |
getGeneSetNetworks | Generate geneset networks from an annotated network. |
getGeneSets | Generate genesets from an annotated network. |
getPathsAsEIDs | Convert a ranked path list to edge ids of a graph |
KGML2igraph | Processes KGML files into igraph objects |
layoutVertexByAttr | A graph layout function, which groups vertices by attribute. |
makeGeneNetwork | Expand reactions / complexes into their gene constituents. |
makeMetaboliteNetwork | Convert metabolic network to metabolite network. |
makeReactionNetwork | Convert metabolic network to reaction network. |
MIRIAM | MIRIAM annotation attributes |
NetPathMiner-package | General framework for network extraction, path mining. |
NPMdefaults | Default values for NetPathMiner |
pathClassifier | HME3M Markov pathway classifier. |
pathCluster | 3M Markov mixture model for clustering pathways |
pathRanker | Extracting and ranking paths from a network |
pathsToBinary | Converts the result from pathRanker into something suitable... |
plotAllNetworks | Higlighting ranked paths over multiple network... |
plotClassifierROC | Diagnostic plots for pathClassifier. |
plotClusters | Plots the structure of all path clusters |
plotCytoscape | Plots an annotated igraph object in Cytoscape. |
plotNetwork | Plots an annotated igraph object. |
plotPathClassifier | Plots the structure of specified path found by... |
plotPathCluster | Plots the structure of specified path cluster |
plotPaths | Plots an annotated igraph object higlighting ranked paths. |
predictPathClassifier | Predicts new paths given a pathClassifier model. |
predictPathCluster | Predicts new paths given a pathCluster model |
registerMemoryErr | Internal method to register memery errors. |
reindexNetwork | Replaces current vertex ids with chosen attribute. |
rmSmallCompounds | Remove uniquitous compounds from a metabolic network |
samplePaths | Creates a set of sample path p-values for each length given a... |
SBML2igraph | Processes SBML files into igraph objects |
simplifyReactionNetwork | Removes reactions with no gene annotations |
toGraphNEL | Converts an annotated igraph object to graphNEL |
vertexDeleteReconnect | Network editing: removing vertices and connecting their... |
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