TCGA_mutations          TCGA mutational profiles across 12 major cancer
                        types from Kandoth et al. (2013)
dBUMfit                 Function to fit a p-value distribution under
                        beta-uniform mixture model
dBUMscore               Function to transform p-values into scores
                        according to the fitted beta-uniform mixture
                        model and/or after controlling false discovery
                        rate
dCheckParallel          Function to check whether parallel computing
                        should be used and how
dCommSignif             Function to test the significance of
                        communities within a graph
dContrast               Function to help build the contrast matrix
dDAGancestor            Function to find common ancestors of two
                        terms/nodes from a direct acyclic graph (DAG)
dDAGannotate            Function to generate a subgraph of a direct
                        acyclic graph (DAG) induced by the input
                        annotation data
dDAGgeneSim             Function to calculate pair-wise semantic
                        similarity between genes based on a direct
                        acyclic graph (DAG) with annotated data
dDAGinduce              Function to generate a subgraph of a direct
                        acyclic graph (DAG) induced by given vertices
dDAGlevel               Function to define/calculate the level of nodes
                        in a direct acyclic graph (DAG)
dDAGreverse             Function to reverse the edge direction of a
                        direct acyclic graph (DAG)
dDAGroot                Function to find the root node of a direct
                        acyclic graph (DAG)
dDAGtermSim             Function to calculate pair-wise semantic
                        similarity between input terms based on a
                        direct acyclic graph (DAG) with annotated data
dDAGtip                 Function to find the tip node(s) of a direct
                        acyclic graph (DAG)
dEnricher               Function to conduct enrichment analysis given
                        the input data and the ontology in query
dEnricherView           Function to view enrichment results of
                        dEnricher
dFDRscore               Function to transform fdr into scores according
                        to log-likelihood ratio between the true
                        positives and the false positivies and/or after
                        controlling false discovery rate
dGSEA                   Function to conduct gene set enrichment
                        analysis given the input data and the ontology
                        in query
dGSEAview               Function to view enrichment results in a
                        sample-specific manner
dGSEAwrite              Function to write out enrichment results
dNetConfidence          Function to append the confidence information
                        from the source graphs into the target graph
dNetFind                Function to find heuristically maximum scoring
                        subgraph
dNetInduce              Function to generate a subgraph induced by
                        given vertices and their k nearest neighbors
dNetPipeline            Function to setup the pipeline for finding
                        maximum-scoring subgraph from an input graph
                        and the signficance imposed on its nodes
dNetReorder             Function to reorder the multiple graph
                        colorings within a sheet-shape rectangle grid
dPvalAggregate          Function to aggregate p values
dRDataLoader            Function to load dnet built-in RData
dRWR                    Function to implement Random Walk with Restart
                        (RWR) on the input graph
dRWRcontact             Function to estimate RWR-based contact strength
                        between samples from an input gene-sample data
                        matrix, an input graph and its pre-computed
                        affinity matrix
dRWRpipeline            Function to setup a pipeine to estimate
                        RWR-based contact strength between samples from
                        an input gene-sample data matrix and an input
                        graph
dSVDsignif              Function to obtain SVD-based gene significance
                        from the input gene-sample matrix
ig.HPPA                 Human Phenotype Phenotypic Abnormality (HPPA).
org.Hs.egHPPA           Annotations of Human Entrez Genes (EG) by Human
                        Phenotype Phenotypic Abnormality (HPPA).
org.Hs.string900        Human functional protein association network
                        from STRING with highest confidence (no less
                        than 900).
visBoxplotAdv           Function to visualise a data frame using
                        advanced boxplot
visDAG                  Function to visualise a direct acyclic graph
                        (DAG) with node colorings according to a named
                        input data vector (if provided)
visGSEA                 Function to visualise running enrichment score
                        for a given sample and a gene set
visNet                  Function to visualise a graph object of class
                        "igraph" or "graphNEL"
visNetArc               Function to visualise an igraph object via arc
                        diagram
visNetCircle            Function to visualise an igraph object via
                        circle diagram
visNetMul               Function to visualise the same graph but with
                        multiple graph node colorings according to
                        input data matrix
visNetReorder           Function to visualise the multiple graph
                        colorings reorded within a sheet-shape
                        rectangle grid
