KGML2igraph             Processes KGML files into igraph objects
NPMdefaults             Default values for NetPathMiner
NetPathMiner-package    General framework for network extraction, path
                        mining.
SBML2igraph             Processes SBML files into igraph objects
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
expandComplexes         Expand reactions / complexes into their gene
                        constituents.
extractPathNetwork      Creates a subnetwork from a ranked path list
getAttrStatus           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
layoutVertexByAttr      A graph layout function, which groups vertices
                        by attribute.
makeMetaboliteNetwork   Convert metabolic network to metabolite
                        network.
makeReactionNetwork     Convert metabolic network to reaction network.
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 for pathClassifier or
                        pathCluster.
plotAllNetworks         Higlighting ranked paths over multiple network
                        representations.
plotClassifierROC       Diagnostic plots for pathClassifier.
plotClusterMatrix       Plots the structure of all path clusters
plotCytoscapeGML        Plots an annotated igraph object in Cytoscape.
plotNetwork             Plots an annotated igraph object.
plotPathClassifier      Plots the structure of specified path found by
                        pathClassifier.
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 weighted network
simplifyReactionNetwork
                        Removes reactions with no gene annotations
stdAttrNames            MIRIAM annotation attributes
toGraphNEL              Converts an annotated igraph object to graphNEL
vertexDeleteReconnect   Network editing: removing vertices and
                        connecting their neighbours
