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

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.

AuthorHai Fang and Julian Gough
Date of publication2016-05-31 17:43:49
MaintainerHai Fang <hfang@well.ox.ac.uk>
LicenseGPL-2
Version1.0.9
http://supfam.org/dnet
http://cran.r-project.org/package=dnet, http://dnet.r-forge.r-project.org, https://github.com/hfang-bristol/dnet

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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