dnet: Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology
Version 1.0.10

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
Bioconductor views Bioinformatics
Date of publication2017-01-27 10:18:05
MaintainerHai Fang <hfang@well.ox.ac.uk>
LicenseGPL-2
Version1.0.10
URL http://dnet.r-forge.r-project.org https://github.com/hfang-bristol/dnet http://supfam.org/dnet
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("dnet")

Popular man pages

dDAGinduce: Function to generate a subgraph of a direct acyclic graph...
dDAGreverse: Function to reverse the edge direction of a direct acyclic...
dDAGroot: Function to find the root node of a direct acyclic graph...
dNetFind: Function to find heuristically maximum scoring subgraph
dRWR: Function to implement Random Walk with Restart (RWR) on the...
visDAG: Function to visualise a direct acyclic graph (DAG) with node...
visNetArc: Function to visualise an igraph object via arc diagram
See all...

All man pages Function index File listing

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...

Functions

TCGA_mutations Man page
dBUMfit Man page Source code
dBUMscore Man page Source code
dCheckParallel Man page Source code
dCommSignif Man page Source code
dContrast Man page Source code
dDAGancestor Man page Source code
dDAGannotate Man page Source code
dDAGgeneSim Man page Source code
dDAGinduce Man page Source code
dDAGlevel Man page Source code
dDAGreverse Man page Source code
dDAGroot Man page Source code
dDAGtermSim Man page Source code
dDAGtip Man page Source code
dEnricher Man page Source code
dEnricherView Man page Source code
dFDRscore Man page Source code
dFunArgs Man page Source code
dGSEA Man page Source code
dGSEAview Man page Source code
dGSEAwrite Man page Source code
dNetConfidence Man page Source code
dNetFind Man page Source code
dNetInduce Man page Source code
dNetPipeline Man page Source code
dNetReorder Man page Source code
dPvalAggregate Man page Source code
dRDataLoader Man page Source code
dRWR Man page Source code
dRWRcontact Man page Source code
dRWRpipeline Man page Source code
dSVDsignif Man page Source code
ig.HPPA Man page
org.Hs.egHPPA Man page
visBoxplotAdv Man page Source code
visDAG Man page Source code
visGSEA Man page Source code
visNet Man page Source code
visNetAnimate Man page Source code
visNetArc Man page Source code
visNetCircle Man page Source code
visNetMul Man page Source code
visNetReorder Man page Source code

Files

inst
inst/staticdocs
inst/staticdocs/RData.md
inst/staticdocs/images
inst/staticdocs/images/dnet_logo.png
inst/staticdocs/images/dnet_logo1.png
inst/staticdocs/images/dnet_logo2.png
inst/staticdocs/images/dnet_workflow.png
inst/staticdocs/images/dnet_userIO.png
inst/staticdocs/faq
inst/staticdocs/faq/FAQ5.r
inst/staticdocs/faq/List_faqs.txt
inst/staticdocs/faq/FAQ2.r
inst/staticdocs/faq/FAQ1.r
inst/staticdocs/faq/FAQ6.r
inst/staticdocs/faq/FAQ4.r
inst/staticdocs/faq/FAQ3.r
inst/staticdocs/INSTALLATIONs_tmp.md
inst/staticdocs/demo
inst/staticdocs/demo/List_demos.txt
inst/staticdocs/demo/Fang.r
inst/staticdocs/demo/TCGA_pre.r
inst/staticdocs/demo/Hiratani.r
inst/staticdocs/demo/TCGA.r
inst/staticdocs/demo/CLL.r
inst/staticdocs/demo/Hiratani_pre.r
inst/staticdocs/demo/ALL.r
inst/staticdocs/README.md
inst/staticdocs/INSTALLATIONs.md
inst/staticdocs/README_tmp.md
inst/staticdocs/templates
inst/staticdocs/templates/navbar.html
inst/staticdocs/templates/footer.html
inst/staticdocs/RData_tmp.md
inst/staticdocs/docs.r
inst/staticdocs/CITATIONs.md
inst/CITATION
inst/NEWS
NAMESPACE
data
data/org.Hs.egHPPA.RData
data/TCGA_mutations.RData
data/datalist
data/ig.HPPA.RData
R
R/visNetMul.r
R/dBUMscore.r
R/dDAGannotate.r
R/dRDataLoader.r
R/dFunArgs.r
R/dDAGgeneSim.r
R/visNet.r
R/dCheckParallel.r
R/dDAGlevel.r
R/dRWR.r
R/visNetArc.r
R/dNetReorder.r
R/dRWRcontact.r
R/dDAGancestor.r
R/dNetInduce.r
R/dDAGtip.r
R/dCommSignif.r
R/dPvalAggregate.r
R/dSVDsignif.r
R/dDAGinduce.r
R/dContrast.r
R/visBoxplotAdv.r
R/dDAGreverse.r
R/dBUMfit.r
R/dGSEAwrite.r
R/dEnricher.r
R/dNetFind.r
R/dGSEA.r
R/visNetAnimate.r
R/dRWRpipeline.r
R/visNetReorder.r
R/visGSEA.r
R/dGSEAview.r
R/visDAG.r
R/dFDRscore.r
R/dDAGtermSim.r
R/visNetCircle.r
R/dNetConfidence.r
R/dEnricherView.r
R/dDAGroot.r
R/dNetPipeline.r
MD5
DESCRIPTION
man
man/visGSEA.Rd
man/dFDRscore.Rd
man/visNetReorder.Rd
man/dRWR.Rd
man/dEnricherView.Rd
man/visNetMul.Rd
man/dNetPipeline.Rd
man/dRWRcontact.Rd
man/dDAGgeneSim.Rd
man/dCommSignif.Rd
man/dEnricher.Rd
man/dBUMfit.Rd
man/visNetCircle.Rd
man/dGSEAview.Rd
man/TCGA_mutations.Rd
man/dGSEAwrite.Rd
man/dNetConfidence.Rd
man/dDAGtip.Rd
man/dNetInduce.Rd
man/org.Hs.egHPPA.Rd
man/visDAG.Rd
man/dCheckParallel.Rd
man/dNetFind.Rd
man/dPvalAggregate.Rd
man/visNet.Rd
man/ig.HPPA.Rd
man/dRDataLoader.Rd
man/dFunArgs.Rd
man/visBoxplotAdv.Rd
man/dBUMscore.Rd
man/dDAGancestor.Rd
man/dDAGlevel.Rd
man/dRWRpipeline.Rd
man/dSVDsignif.Rd
man/dContrast.Rd
man/dDAGinduce.Rd
man/dDAGroot.Rd
man/dDAGtermSim.Rd
man/dDAGreverse.Rd
man/visNetAnimate.Rd
man/visNetArc.Rd
man/dDAGannotate.Rd
man/dNetReorder.Rd
man/dGSEA.Rd
dnet documentation built on May 19, 2017, 9:56 a.m.

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