dnet: Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology

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The focus of the dnet is to make sense of omics data (such as gene expression and mutations) from different angles including: integration with molecular networks, enrichments using ontologies, and relevance to gene evolutionary ages. Integration is achieved to identify a gene subnetwork from the whole gene network whose nodes/genes are labelled with informative data (such as the significant levels of differential expression or survival risks). To help make sense of identified gene 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 calculating semantic similarity between ontology terms (and between genes) and for calculating network affinity based on random walk; both can be done via high-performance parallel computing.

Author
Hai Fang and Julian Gough
Date of publication
2016-05-31 17:43:49
Maintainer
Hai Fang <hfang@well.ox.ac.uk>
License
GPL-2
Version
1.0.9
URLs

View on CRAN

Man pages

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
Annotations of Human Entrez Genes (EG) by Human Phenotype...
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...

Files in this package

dnet
dnet/inst
dnet/inst/staticdocs
dnet/inst/staticdocs/RData.md
dnet/inst/staticdocs/images
dnet/inst/staticdocs/images/dnet_logo.png
dnet/inst/staticdocs/images/dnet_logo1.png
dnet/inst/staticdocs/images/dnet_logo2.png
dnet/inst/staticdocs/images/dnet_workflow.png
dnet/inst/staticdocs/images/dnet_userIO.png
dnet/inst/staticdocs/faq
dnet/inst/staticdocs/faq/FAQ5.r
dnet/inst/staticdocs/faq/List_faqs.txt
dnet/inst/staticdocs/faq/FAQ2.r
dnet/inst/staticdocs/faq/FAQ1.r
dnet/inst/staticdocs/faq/FAQ6.r
dnet/inst/staticdocs/faq/FAQ4.r
dnet/inst/staticdocs/faq/FAQ3.r
dnet/inst/staticdocs/INSTALLATIONs_tmp.md
dnet/inst/staticdocs/demo
dnet/inst/staticdocs/demo/List_demos.txt
dnet/inst/staticdocs/demo/Fang.r
dnet/inst/staticdocs/demo/TCGA_pre.r
dnet/inst/staticdocs/demo/Hiratani.r
dnet/inst/staticdocs/demo/TCGA.r
dnet/inst/staticdocs/demo/CLL.r
dnet/inst/staticdocs/demo/Hiratani_pre.r
dnet/inst/staticdocs/demo/ALL.r
dnet/inst/staticdocs/README.md
dnet/inst/staticdocs/INSTALLATIONs.md
dnet/inst/staticdocs/README_tmp.md
dnet/inst/staticdocs/templates
dnet/inst/staticdocs/templates/navbar.html
dnet/inst/staticdocs/templates/footer.html
dnet/inst/staticdocs/RData_tmp.md
dnet/inst/staticdocs/docs.r
dnet/inst/staticdocs/CITATIONs.md
dnet/inst/CITATION
dnet/inst/NEWS
dnet/NAMESPACE
dnet/data
dnet/data/org.Hs.egHPPA.RData
dnet/data/TCGA_mutations.RData
dnet/data/datalist
dnet/data/ig.HPPA.RData
dnet/R
dnet/R/visNetMul.r
dnet/R/dBUMscore.r
dnet/R/dDAGannotate.r
dnet/R/dRDataLoader.r
dnet/R/dFunArgs.r
dnet/R/dDAGgeneSim.r
dnet/R/visNet.r
dnet/R/dCheckParallel.r
dnet/R/dDAGlevel.r
dnet/R/dRWR.r
dnet/R/visNetArc.r
dnet/R/dNetReorder.r
dnet/R/dRWRcontact.r
dnet/R/dDAGancestor.r
dnet/R/dNetInduce.r
dnet/R/dDAGtip.r
dnet/R/dCommSignif.r
dnet/R/dPvalAggregate.r
dnet/R/dSVDsignif.r
dnet/R/dDAGinduce.r
dnet/R/dContrast.r
dnet/R/visBoxplotAdv.r
dnet/R/dDAGreverse.r
dnet/R/dBUMfit.r
dnet/R/dGSEAwrite.r
dnet/R/dEnricher.r
dnet/R/dNetFind.r
dnet/R/dGSEA.r
dnet/R/visNetAnimate.r
dnet/R/dRWRpipeline.r
dnet/R/visNetReorder.r
dnet/R/visGSEA.r
dnet/R/dGSEAview.r
dnet/R/visDAG.r
dnet/R/dFDRscore.r
dnet/R/dDAGtermSim.r
dnet/R/visNetCircle.r
dnet/R/dNetConfidence.r
dnet/R/dEnricherView.r
dnet/R/dDAGroot.r
dnet/R/dNetPipeline.r
dnet/MD5
dnet/DESCRIPTION
dnet/man
dnet/man/visGSEA.Rd
dnet/man/dFDRscore.Rd
dnet/man/visNetReorder.Rd
dnet/man/dRWR.Rd
dnet/man/dEnricherView.Rd
dnet/man/visNetMul.Rd
dnet/man/dNetPipeline.Rd
dnet/man/dRWRcontact.Rd
dnet/man/dDAGgeneSim.Rd
dnet/man/dCommSignif.Rd
dnet/man/dEnricher.Rd
dnet/man/dBUMfit.Rd
dnet/man/visNetCircle.Rd
dnet/man/dGSEAview.Rd
dnet/man/TCGA_mutations.Rd
dnet/man/dGSEAwrite.Rd
dnet/man/dNetConfidence.Rd
dnet/man/dDAGtip.Rd
dnet/man/dNetInduce.Rd
dnet/man/org.Hs.egHPPA.Rd
dnet/man/visDAG.Rd
dnet/man/dCheckParallel.Rd
dnet/man/dNetFind.Rd
dnet/man/dPvalAggregate.Rd
dnet/man/visNet.Rd
dnet/man/ig.HPPA.Rd
dnet/man/dRDataLoader.Rd
dnet/man/dFunArgs.Rd
dnet/man/visBoxplotAdv.Rd
dnet/man/dBUMscore.Rd
dnet/man/dDAGancestor.Rd
dnet/man/dDAGlevel.Rd
dnet/man/dRWRpipeline.Rd
dnet/man/dSVDsignif.Rd
dnet/man/dContrast.Rd
dnet/man/dDAGinduce.Rd
dnet/man/dDAGroot.Rd
dnet/man/dDAGtermSim.Rd
dnet/man/dDAGreverse.Rd
dnet/man/visNetAnimate.Rd
dnet/man/visNetArc.Rd
dnet/man/dDAGannotate.Rd
dnet/man/dNetReorder.Rd
dnet/man/dGSEA.Rd