DNET: dynamic networks via an integrative analysis of biological
networks and high-throughput digitised data
The 'dnet' package is initiated to fill in the need of an open-source tool for analysing biological networks and high-throughput biological data in an integrative manner. More specifically, dnet intends to analyse the biological network whose nodes/genes are associated with digitised information such as expression levels across samples. Also, dnet aims to deliver an eye-intuitive tool for network-based sample stratifications.
'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' 'visColormap.r' 'visColoralpha.r'
'visHeatmap.r' 'visHeatmapAdv.r' 'visTreeBootstrap.r'

Dynamic NETworks via integrative analysis of digitised data in
terms of network, ontology and evolution
The 'dnet' package is initiated to fill in the need of an open-source tool for digitised data in an integrative manner. 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 age information in major organisms including human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. 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' 'dContrast.r' 'dCommSignif.r'
'dSVDsignif.r' 'dFDRscore.r' 'visColormap.r' 'visColoralpha.r'
'visHeatmap.r' 'visHeatmapAdv.r' 'visTreeBootstrap.r'
'dDAGinduce.r' 'dDAGreverse.r' 'dDAGroot.r' 'dDAGtip.r'
'dDAGlevel.r' 'dDAGannotate.r' 'visDAG.r' 'dEnricher.r'