Integrative analysis of digitised data in terms of network,
ontology and evolution
'dGSEA.r' 'dGSEAview.r' 'dGSEAwrite.r' 'visGSEA.r'
'dPvalAggregate.r' 'dNetInduce.r' 'dBUMfit.r' 'dBUMscore.r'
'dNetFind.r' 'dNetPipeline.r' 'dNetConfidence.r' 'visNet.r'
'visNetMul.r' 'visNetReorder.r' 'dNetReorder.r' 'visNetArc.r'
'visNetCircle.r' 'dRWR.r' 'dContrast.r' 'dCommSignif.r'
'dSVDsignif.r' 'dFDRscore.r' 'dDAGinduce.r' 'dDAGreverse.r'
'dDAGroot.r' 'dDAGtip.r' 'dDAGlevel.r' 'dDAGannotate.r'
'visDAG.r' 'dEnricher.r' 'dEnricherView.r' 'visBoxplotAdv.r'
'dRDataLoader.r'

an open-source R package for omics data integrative analysis in
terms of network, evolution and ontology
The 'dnet' package is initiated to fill in the need of an open-source tool for high-throughput omics data in an integrative manner in terms of network, evolution and ontology. More specifically, dnet intends to analyse the biological network whose nodes/genes are associated with digitised information such as expression levels across samples. To help make sense of identified networks, enrichment analysis is also supported using a wide variety of pre-compiled ontologies and phylostratific gene age information in major organisms including human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. Add-on functionalities are supports for semantic similarity calculation between ontology terms (and genes), and network affinity calculation using Random Walk with Restart; both can be done via high-performance parallel computing. In summary, dnet aims to deliver an eye-intuitive tool with rich visuals but less inputs.
'dGSEA.r' 'dGSEAview.r' 'dGSEAwrite.r' 'visGSEA.r'
'dPvalAggregate.r' 'dNetInduce.r' 'dBUMfit.r' 'dBUMscore.r'
'dNetFind.r' 'dNetPipeline.r' 'dNetConfidence.r' 'visNet.r'
'visNetMul.r' 'visNetReorder.r' 'dNetReorder.r' 'visNetArc.r'
'visNetCircle.r' 'dRWR.r' 'dRWRcontact.r' 'dRWRpipeline.r'
'dContrast.r' 'dCommSignif.r' 'dSVDsignif.r' 'dFDRscore.r'
'dDAGinduce.r' 'dDAGreverse.r' 'dDAGroot.r' 'dDAGtip.r'
'dDAGlevel.r' 'dDAGannotate.r' 'dDAGancestor.r' 'dDAGtermSim.r'
'dDAGgeneSim.r' 'visDAG.r' 'dEnricher.r' 'dEnricherView.r'
'visBoxplotAdv.r' 'dRDataLoader.r' 'dCheckParallel.r'