dcGOR: Analysis of Ontologies and Protein Domain Annotations

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.

AuthorHai Fang and Julian Gough
Date of publication2015-07-27 10:52:03
MaintainerHai Fang <hfang@well.ox.ac.uk>
LicenseGPL-2
Version1.0.6
http://supfam.org/dcGOR
http://cran.r-project.org/package=dcGOR, http://dcgor.r-forge.r-project.org, https://github.com/hfang-bristol/dcGOR

View on CRAN

Man pages

AdjData-class: Definition for VIRTUAL S4 class AdjData

Ancestral_domainome: Ancestral superfamily domain repertoires in Eukaryotes

Anno-class: Definition for S4 class Anno

AnnoData-class: Definition for VIRTUAL S4 class AnnoData

Anno-method: Methods defined for S4 class Anno

Cnetwork-class: Definition for S4 class Cnetwork

Cnetwork-method: Methods defined for S4 class Cnetwork

Coutput-class: Definition for S4 class Coutput

Coutput-method: Methods defined for S4 class Coutput

dcAlgo: Function to apply dcGO algorithm to infer domain-centric...

dcAlgoPredict: Function to predict ontology terms given domain architectures...

dcAlgoPredictGenome: Function to predict ontology terms for genomes with domain...

dcAlgoPredictMain: Function to predict ontology terms given an input file...

dcAlgoPredictPR: Function to assess the prediction performance via...

dcAlgoPropagate: Function to propagate ontology annotations according to an...

dcAncestralML: Function to reconstruct ancestral discrete states using fast...

dcAncestralMP: Function to reconstruct ancestral discrete states using...

dcBuildAnno: Function to build an object of the S4 class Anno from input...

dcBuildInfoDataFrame: Function to build an object of the S4 class InfoDataframe...

dcBuildOnto: Function to build an object of the S4 class Onto from input...

dcConverter: Function to convert an object between graph classes

dcDAGannotate: Function to generate a subgraph of a direct acyclic graph...

dcDAGdomainSim: Function to calculate pair-wise semantic similarity between...

dcDuplicated: Function to determine the duplicated patterns from input data...

dcEnrichment: Function to conduct ontology enrichment analysis given a...

dcFunArgs: Function to assign (and evaluate) arguments with default...

dcList2Matrix: Function to convert a list into a matrix containing three...

dcNaivePredict: Function to perform naive prediction from input known...

dcRDataLoader: Function to load dcGOR built-in RData

dcRWRpipeline: Function to setup a pipeine to estimate RWR-based contact...

dcRWRpredict: Function to perform RWR-based ontology term predictions from...

dcSparseMatrix: Function to create a sparse matrix for an input file with...

dcSplitArch: Function to obtain a list of features via splitting an input...

dcSubtreeClade: Function to extract a subtree under a given clade from a...

dcSubtreeTips: Function to extract a tip-induced subtree from a...

dcSupraBetter: Function to find supra-domains with better scores than their...

dcTreeConnectivity: Function to calculate the sparse connectivity matrix between...

Dnetwork-class: Definition for S4 class Dnetwork

Dnetwork-method: Methods defined for S4 class Dnetwork

Eoutput-class: Definition for S4 class Eoutput

Eoutput-method: Methods defined for S4 class Eoutput

eTOL: eukaryotic Tree Of Life (eTOL)

InfoDataFrame-class: Definition for S4 class InfoDataFrame

InfoDataFrame-method: Methods defined for S4 class InfoDataFrame

InterPro: InterPro domains (InterPro).

InterPro2GOBP: Annotations of InterPro domains by Gene Ontology Biological...

InterPro2GOCC: Annotations of InterPro domains by Gene Ontology Cellular...

InterPro2GOMF: Annotations of InterPro domains by Gene Ontology Molecular...

Onto-class: Definition for S4 class Onto

onto.DO: Disease Ontology (DO).

onto.GOBP: Gene Ontology Biological Process (GOBP).

onto.GOCC: Gene Ontology Cellular Component (GOCC).

onto.GOMF: Gene Ontology Molecular Function (GOMF).

onto.HPMI: Human Phenotype Mode of Inheritance (HPMI).

onto.HPON: Human Phenotype ONset and clinical course (HPON).

onto.HPPA: Human Phenotype Phenotypic Abnormality (HPPA).

Onto-method: Methods defined for S4 class Onto

onto.MP: Mammalian Phenotype (MP).

Pfam: Pfam domains (Pfam).

Pfam2GOBP: Annotations of Pfam domains by Gene Ontology Biological...

Pfam2GOCC: Annotations of Pfam domains by Gene Ontology Cellular...

Pfam2GOMF: Annotations of Pfam domains by Gene Ontology Molecular...

Rfam: RNA families (Rfam).

Rfam2GOBP: Annotations of Rfam RNA families by Gene Ontology Biological...

Rfam2GOCC: Annotations of Rfam RNA families by Gene Ontology Cellular...

Rfam2GOMF: Annotations of Rfam RNA families by Gene Ontology Molecular...

SCOP.fa: SCOP domain families (fa).

SCOP.fa2DO: Annotations of SCOP domain families (fa) by Disease Ontology...

SCOP.fa2GOBP: Annotations of SCOP domain families (fa) by Gene Ontology...

SCOP.fa2GOCC: Annotations of SCOP domain families (fa) by Gene Ontology...

SCOP.fa2GOMF: Annotations of SCOP domain families (fa) by Gene Ontology...

SCOP.fa2HPMI: Annotations of SCOP domain families (fa) by Human Phenotype...

SCOP.fa2HPON: Annotations of SCOP domain families (fa) by Human Phenotype...

SCOP.fa2HPPA: Annotations of SCOP domain families (fa) by Human Phenotype...

SCOP.fa2MP: Annotations of SCOP domain families (fa) by Mammalian...

SCOP.sf: SCOP domain superfamilies (sf).

SCOP.sf2DO: Annotations of SCOP domain superfamilies (sf) by Disease...

SCOP.sf2GOBP: Annotations of SCOP domain superfamilies (sf) by Gene...

SCOP.sf2GOCC: Annotations of SCOP domain superfamilies (sf) by Gene...

SCOP.sf2GOMF: Annotations of SCOP domain superfamilies (sf) by Gene...

SCOP.sf2HPMI: Annotations of SCOP domain superfamilies (sf) by Human...

SCOP.sf2HPON: Annotations of SCOP domain superfamilies (sf) by Human...

SCOP.sf2HPPA: Annotations of SCOP domain superfamilies (sf) by Human...

SCOP.sf2MP: Annotations of SCOP domain superfamilies (sf) by Mammalian...

visEnrichment: Function to visualise enrichment analysis outputs in the...

Files in this package

dcGOR
dcGOR/inst
dcGOR/inst/staticdocs
dcGOR/inst/staticdocs/RData.md
dcGOR/inst/staticdocs/images
dcGOR/inst/staticdocs/images/dcGOR_logo.png
dcGOR/inst/staticdocs/images/dcGOR_workflow.png
dcGOR/inst/staticdocs/faq
dcGOR/inst/staticdocs/faq/List_faqs.txt
dcGOR/inst/staticdocs/demo
dcGOR/inst/staticdocs/demo/Customisation.r
dcGOR/inst/staticdocs/demo/List_demos.txt
dcGOR/inst/staticdocs/demo/Basu.r
dcGOR/inst/staticdocs/demo/Fang.r
dcGOR/inst/staticdocs/demo/AlgoPred.r
dcGOR/inst/staticdocs/demo/Fang_paper.r
dcGOR/inst/staticdocs/README.md
dcGOR/inst/staticdocs/INSTALLATIONs.md
dcGOR/inst/staticdocs/templates
dcGOR/inst/staticdocs/templates/navbar.html
dcGOR/inst/staticdocs/templates/footer.html
dcGOR/inst/staticdocs/docs.r
dcGOR/inst/staticdocs/CITATIONs.md
dcGOR/inst/CITATION
dcGOR/inst/NEWS
dcGOR/NAMESPACE
dcGOR/data
dcGOR/data/onto.GOBP.RData
dcGOR/data/Rfam.RData
dcGOR/data/InterPro2GOBP.RData
dcGOR/data/onto.HPMI.RData
dcGOR/data/onto.DO.RData
dcGOR/data/InterPro2GOMF.RData
dcGOR/data/SCOP.sf2MP.RData
dcGOR/data/SCOP.sf2HPPA.RData
dcGOR/data/SCOP.sf2GOCC.RData
dcGOR/data/SCOP.fa2HPPA.RData
dcGOR/data/Ancestral_domainome.RData
dcGOR/data/eTOL.RData
dcGOR/data/SCOP.fa2HPON.RData
dcGOR/data/onto.HPON.RData
dcGOR/data/SCOP.fa2DO.RData
dcGOR/data/onto.MP.RData
dcGOR/data/SCOP.sf2DO.RData
dcGOR/data/InterPro2GOCC.RData
dcGOR/data/InterPro.RData
dcGOR/data/SCOP.fa.RData
dcGOR/data/SCOP.sf2HPON.RData
dcGOR/data/Pfam2GOCC.RData
dcGOR/data/SCOP.sf2HPMI.RData
dcGOR/data/SCOP.fa2GOBP.RData
dcGOR/data/datalist
dcGOR/data/SCOP.fa2GOCC.RData
dcGOR/data/Rfam2GOBP.RData
dcGOR/data/onto.GOMF.RData
dcGOR/data/SCOP.sf2GOBP.RData
dcGOR/data/Rfam2GOCC.RData
dcGOR/data/SCOP.sf.RData
dcGOR/data/SCOP.fa2MP.RData
dcGOR/data/Rfam2GOMF.RData
dcGOR/data/SCOP.fa2HPMI.RData
dcGOR/data/SCOP.sf2GOMF.RData
dcGOR/data/Pfam2GOBP.RData
dcGOR/data/onto.HPPA.RData
dcGOR/data/Pfam2GOMF.RData
dcGOR/data/onto.GOCC.RData
dcGOR/data/SCOP.fa2GOMF.RData
dcGOR/data/Pfam.RData
dcGOR/R
dcGOR/R/dcAlgoPredictGenome.r
dcGOR/R/dcAncestralML.r
dcGOR/R/visEnrichment.r
dcGOR/R/dcFunArgs.r
dcGOR/R/dcList2Matrix.r
dcGOR/R/dcSplitArch.r
dcGOR/R/dcAlgoPredictPR.r
dcGOR/R/dcBuildInfoDataFrame.r
dcGOR/R/dcSparseMatrix.r
dcGOR/R/dcConverter.r
dcGOR/R/dcRDataLoader.r
dcGOR/R/dcNaivePredict.r
dcGOR/R/dcDAGannotate.r
dcGOR/R/dcDAGdomainSim.r
dcGOR/R/dcRWRpipeline.r
dcGOR/R/dcSubtreeClade.r
dcGOR/R/ClassMethod-dcGOR.r
dcGOR/R/dcRWRpredict.r
dcGOR/R/dcBuildAnno.r
dcGOR/R/dcAlgo.r
dcGOR/R/dcSupraBetter.r
dcGOR/R/dcAlgoPredict.r
dcGOR/R/dcEnrichment.r
dcGOR/R/dcAncestralMP.r
dcGOR/R/dcDuplicated.r
dcGOR/R/dcAlgoPredictMain.r
dcGOR/R/dcBuildOnto.r
dcGOR/R/dcTreeConnectivity.r
dcGOR/R/dcAlgoPropagate.r
dcGOR/R/dcSubtreeTips.r
dcGOR/MD5
dcGOR/DESCRIPTION
dcGOR/man
dcGOR/man/Anno-class.Rd dcGOR/man/onto.DO.Rd dcGOR/man/dcRWRpredict.Rd dcGOR/man/Dnetwork-class.Rd dcGOR/man/dcAlgoPredict.Rd dcGOR/man/dcSplitArch.Rd dcGOR/man/dcSubtreeTips.Rd dcGOR/man/dcRDataLoader.Rd dcGOR/man/InterPro2GOCC.Rd dcGOR/man/dcBuildOnto.Rd dcGOR/man/Rfam.Rd dcGOR/man/SCOP.sf2HPMI.Rd dcGOR/man/Rfam2GOCC.Rd dcGOR/man/AdjData-class.Rd dcGOR/man/SCOP.fa2GOBP.Rd dcGOR/man/onto.GOCC.Rd dcGOR/man/SCOP.sf2MP.Rd dcGOR/man/SCOP.fa2HPPA.Rd dcGOR/man/onto.HPPA.Rd dcGOR/man/SCOP.fa2GOMF.Rd dcGOR/man/AnnoData-class.Rd dcGOR/man/dcAncestralMP.Rd dcGOR/man/onto.MP.Rd dcGOR/man/Coutput-method.Rd dcGOR/man/Eoutput-class.Rd dcGOR/man/dcDuplicated.Rd dcGOR/man/Anno-method.Rd dcGOR/man/visEnrichment.Rd dcGOR/man/SCOP.fa.Rd dcGOR/man/onto.GOBP.Rd dcGOR/man/dcBuildAnno.Rd dcGOR/man/InfoDataFrame-method.Rd dcGOR/man/onto.HPMI.Rd dcGOR/man/dcFunArgs.Rd dcGOR/man/dcSparseMatrix.Rd dcGOR/man/Ancestral_domainome.Rd dcGOR/man/Pfam2GOMF.Rd dcGOR/man/Eoutput-method.Rd dcGOR/man/InterPro2GOMF.Rd dcGOR/man/dcNaivePredict.Rd dcGOR/man/InterPro2GOBP.Rd dcGOR/man/onto.GOMF.Rd dcGOR/man/InfoDataFrame-class.Rd dcGOR/man/SCOP.fa2GOCC.Rd dcGOR/man/dcSubtreeClade.Rd dcGOR/man/dcEnrichment.Rd dcGOR/man/dcSupraBetter.Rd dcGOR/man/Cnetwork-method.Rd dcGOR/man/SCOP.sf.Rd dcGOR/man/onto.HPON.Rd dcGOR/man/Pfam.Rd dcGOR/man/SCOP.fa2HPON.Rd dcGOR/man/dcConverter.Rd dcGOR/man/Dnetwork-method.Rd dcGOR/man/SCOP.sf2HPON.Rd dcGOR/man/dcAlgoPredictGenome.Rd dcGOR/man/dcAlgoPredictMain.Rd dcGOR/man/Pfam2GOCC.Rd dcGOR/man/Pfam2GOBP.Rd dcGOR/man/dcDAGannotate.Rd dcGOR/man/dcRWRpipeline.Rd dcGOR/man/SCOP.sf2DO.Rd dcGOR/man/SCOP.sf2GOCC.Rd dcGOR/man/dcList2Matrix.Rd dcGOR/man/eTOL.Rd dcGOR/man/dcAlgo.Rd dcGOR/man/SCOP.sf2GOBP.Rd dcGOR/man/dcBuildInfoDataFrame.Rd dcGOR/man/InterPro.Rd dcGOR/man/dcTreeConnectivity.Rd dcGOR/man/dcAlgoPropagate.Rd dcGOR/man/dcAlgoPredictPR.Rd dcGOR/man/Coutput-class.Rd dcGOR/man/SCOP.fa2MP.Rd dcGOR/man/SCOP.sf2GOMF.Rd dcGOR/man/Onto-class.Rd dcGOR/man/Onto-method.Rd dcGOR/man/Rfam2GOBP.Rd dcGOR/man/dcDAGdomainSim.Rd dcGOR/man/Cnetwork-class.Rd dcGOR/man/Rfam2GOMF.Rd dcGOR/man/SCOP.fa2DO.Rd dcGOR/man/SCOP.sf2HPPA.Rd dcGOR/man/dcAncestralML.Rd dcGOR/man/SCOP.fa2HPMI.Rd

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