Package: dnet
Type: Package
Title: Integrative analysis of omics data in terms of network,
        evolution and ontology
Version: 1.0.6
Date: 2014-9-17
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang <hfang@cs.bris.ac.uk>
Depends: R (>= 3.1.0), igraph, supraHex
Imports: graph, Rgraphviz, Matrix, Biobase, foreach, doMC
Suggests: limma, survival
Description: This package is initiated to fill in the need of an open-source tool for high-throughput omics data in an integrative manner in terms of network, evolution and ontology. 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 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
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' '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'
License: GPL-2
biocViews: Bioinformatics
Packaged: 2014-09-17 13:53:16 UTC; hfang
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-17 16:22:46
OS_type: unix
Built: R 3.1.1; ; 2014-09-23 02:54:17 UTC; unix
