Man pages for hfang-bristol/dnet
Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology

dBUMfitFunction to fit a p-value distribution under beta-uniform...
dBUMscoreFunction to transform p-values into scores according to the...
dCheckParallelFunction to check whether parallel computing should be used...
dCommSignifFunction to test the significance of communities within a...
dContrastFunction to help build the contrast matrix
dDAGancestorFunction to find common ancestors of two terms/nodes from a...
dDAGannotateFunction to generate a subgraph of a direct acyclic graph...
dDAGgeneSimFunction to calculate pair-wise semantic similarity between...
dDAGinduceFunction to generate a subgraph of a direct acyclic graph...
dDAGlevelFunction to define/calculate the level of nodes in a direct...
dDAGreverseFunction to reverse the edge direction of a direct acyclic...
dDAGrootFunction to find the root node of a direct acyclic graph...
dDAGtermSimFunction to calculate pair-wise semantic similarity between...
dDAGtipFunction to find the tip node(s) of a direct acyclic graph...
dEnricherFunction to conduct enrichment analysis given the input data...
dEnricherViewFunction to view enrichment results of dEnricher
dFDRscoreFunction to transform fdr into scores according to...
dFunArgsFunction to assign (and evaluate) arguments with default...
dGSEAFunction to conduct gene set enrichment analysis given the...
dGSEAviewFunction to view enrichment results in a sample-specific...
dGSEAwriteFunction to write out enrichment results
dNetConfidenceFunction to append the confidence information from the source...
dNetFindFunction to find heuristically maximum scoring subgraph
dNetInduceFunction to generate a subgraph induced by given vertices and...
dNetPipelineFunction to setup the pipeline for finding maximum-scoring...
dNetReorderFunction to reorder the multiple graph colorings within a...
dPvalAggregateFunction to aggregate p values
dRDataLoaderFunction to load dnet built-in RData
dRWRFunction to implement Random Walk with Restart (RWR) on the...
dRWRcontactFunction to estimate RWR-based contact strength between...
dRWRpipelineFunction to setup a pipeine to estimate RWR-based contact...
dSVDsignifFunction to obtain SVD-based gene significance from the input...
ig.HPPAHuman Phenotype Phenotypic Abnormality (HPPA).
org.Hs.egHPPAAnnotations of Human Entrez Genes (EG) by Human Phenotype...
TCGA_mutationsTCGA mutational profiles across 12 major cancer types from...
visBoxplotAdvFunction to visualise a data frame using advanced boxplot
visDAGFunction to visualise a direct acyclic graph (DAG) with node...
visGSEAFunction to visualise running enrichment score for a given...
visNetFunction to visualise a graph object of class "igraph" or...
visNetAnimateFunction to animate the same graph but with multiple graph...
visNetArcFunction to visualise an igraph object via arc diagram
visNetCircleFunction to visualise an igraph object via circle diagram
visNetMulFunction to visualise the same graph but with multiple graph...
visNetReorderFunction to visualise the multiple graph colorings reorded...
hfang-bristol/dnet documentation built on Aug. 6, 2018, 3:16 a.m.