Package: dcGOR
Type: Package
Title: Analysis of Ontologies and Protein Domain Annotations
Version: 1.0.6
Date: 2015-7-26
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Depends: R (>= 3.1.0), Matrix, igraph, dnet
Imports: methods
Suggests: foreach, doMC, ape
Description: There lacks a package for analysing domain-centric ontologies and annotations, particularly those in the dcGO database. The dcGO (http://supfam.org/SUPERFAMILY/dcGO) is a comprehensive domain-centric database for annotating protein domains using a panel of ontologies including Gene Ontology. With the package, users are expected to analyse and visualise domain-centric ontologies and annotations. Supported analyses include but are not limited to: easy access to a wide range of ontologies and their domain-centric annotations; able to build customised ontologies and annotations; domain-based enrichment analysis and visualisation; construction of a domain (semantic similarity) network according to ontology annotations; significance analysis for estimating a contact (statistical significance) network via Random Walk with Restart; and high-performance parallel computing. The new functionalities are: 1) to create domain-centric ontologies; 2) to predict ontology terms for input protein sequences (precisely domain content in the form of architectures) plus to assess the predictions; 3) to reconstruct ancestral discrete characters using maximum likelihood/parsimony.
URL: http://supfam.org/dcGOR, http://cran.r-project.org/package=dcGOR,
        http://dcgor.r-forge.r-project.org,
        https://github.com/hfang-bristol/dcGOR
Collate: 'ClassMethod-dcGOR.r' 'dcDAGannotate.r' 'dcRDataLoader.r'
        'dcEnrichment.r' 'visEnrichment.r' 'dcDAGdomainSim.r'
        'dcRWRpipeline.r' 'dcConverter.r' 'dcBuildInfoDataFrame.r'
        'dcBuildAnno.r' 'dcBuildOnto.r' 'dcAlgoPropagate.r'
        'dcAlgoPredict.r' 'dcAlgoPredictMain.r' 'dcAlgoPredictGenome.r'
        'dcAncestralML.r' 'dcAncestralMP.r' 'dcSubtreeClade.r'
        'dcSubtreeTips.r' 'dcTreeConnectivity.r' 'dcDuplicated.r'
        'dcSplitArch.r' 'dcAlgo.r' 'dcFunArgs.r' 'dcSparseMatrix.r'
        'dcList2Matrix.r' 'dcAlgoPredictPR.r' 'dcSupraBetter.r'
        'dcRWRpredict.r' 'dcNaivePredict.r'
License: GPL-2
biocViews: Bioinformatics
NeedsCompilation: no
Packaged: 2015-07-26 21:42:57 UTC; hfang
Repository: CRAN
Date/Publication: 2015-07-27 10:52:03
Built: R 3.3.3; ; 2018-04-22 16:35:40 UTC; windows
