Package: dnet
Type: Package
Title: Integrative Analysis of Omics Data in Terms of Network,
        Evolution and Ontology
Version: 1.0.7
Date: 2015-7-17
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Depends: R (>= 3.1.0), igraph, supraHex
Imports: graph, Rgraphviz, Matrix, Biobase
Suggests: limma, survival, foreach, doMC
Description: There lacks an open-source tool for high-throughput omics data in an integrative manner in terms of network, evolution and ontology. To meet this need, 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.
URL: http://supfam.org/dnet, http://dnet.r-forge.r-project.org,
        http://cran.r-project.org/package=dnet,
        https://github.com/hfang-bristol/dnet
Collate: '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' 'visNetAnimate.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' 'dFunArgs.r'
License: GPL-2
biocViews: Bioinformatics
NeedsCompilation: no
Packaged: 2015-07-17 16:02:15 UTC; hfang
Repository: CRAN
Date/Publication: 2015-07-18 00:07:58
