| dBUMfit | Function to fit a p-value distribution under beta-uniform... |
| dBUMscore | Function to transform p-values into scores according to the... |
| dCheckParallel | Function to check whether parallel computing should be used... |
| dCommSignif | Function to test the significance of communities within a... |
| dContrast | Function to help build the contrast matrix |
| dDAGancestor | Function to find common ancestors of two terms/nodes from a... |
| dDAGannotate | Function to generate a subgraph of a direct acyclic graph... |
| dDAGgeneSim | Function to calculate pair-wise semantic similarity between... |
| dDAGinduce | Function to generate a subgraph of a direct acyclic graph... |
| dDAGlevel | Function to define/calculate the level of nodes in a direct... |
| dDAGreverse | Function to reverse the edge direction of a direct acyclic... |
| dDAGroot | Function to find the root node of a direct acyclic graph... |
| dDAGtermSim | Function to calculate pair-wise semantic similarity between... |
| dDAGtip | Function to find the tip node(s) of a direct acyclic graph... |
| dEnricher | Function to conduct enrichment analysis given the input data... |
| dEnricherView | Function to view enrichment results of dEnricher |
| dFDRscore | Function to transform fdr into scores according to... |
| dFunArgs | Function to assign (and evaluate) arguments with default... |
| dGSEA | Function to conduct gene set enrichment analysis given the... |
| dGSEAview | Function to view enrichment results in a sample-specific... |
| dGSEAwrite | Function to write out enrichment results |
| dNetConfidence | Function to append the confidence information from the source... |
| dNetFind | Function to find heuristically maximum scoring subgraph |
| dNetInduce | Function to generate a subgraph induced by given vertices and... |
| dNetPipeline | Function to setup the pipeline for finding maximum-scoring... |
| dNetReorder | Function to reorder the multiple graph colorings within a... |
| 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... |
| dRWRcontact | Function to estimate RWR-based contact strength between... |
| dRWRpipeline | Function to setup a pipeine to estimate RWR-based contact... |
| dSVDsignif | Function to obtain SVD-based gene significance from the input... |
| ig.HPPA | Human Phenotype Phenotypic Abnormality (HPPA). |
| org.Hs.egHPPA | Human Phenotype Phenotypic Abnormality (HPPA). |
| TCGA_mutations | TCGA mutational profiles across 12 major cancer types from... |
| visBoxplotAdv | Function to visualise a data frame using advanced boxplot |
| visDAG | Function to visualise a direct acyclic graph (DAG) with node... |
| visGSEA | Function to visualise running enrichment score for a given... |
| visNet | Function to visualise a graph object of class "igraph" or... |
| visNetAnimate | Function to animate the same graph but with multiple graph... |
| 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... |
| visNetReorder | Function to visualise the multiple graph colorings reorded... |
