Man pages for hfang-bristol/dcGOR
Analysis of Ontologies and Protein Domain Annotations

AdjData-classDefinition for VIRTUAL S4 class AdjData
Ancestral_domainomeAncestral superfamily domain repertoires in Eukaryotes
Anno-classDefinition for S4 class Anno
AnnoData-classDefinition for VIRTUAL S4 class AnnoData
Anno-methodMethods defined for S4 class Anno
Cnetwork-classDefinition for S4 class Cnetwork
Cnetwork-methodMethods defined for S4 class Cnetwork
Coutput-classDefinition for S4 class Coutput
Coutput-methodMethods defined for S4 class Coutput
dcAlgoFunction to apply dcGO algorithm to infer domain-centric...
dcAlgoPredictFunction to predict ontology terms given domain architectures...
dcAlgoPredictGenomeFunction to predict ontology terms for genomes with domain...
dcAlgoPredictMainFunction to predict ontology terms given an input file...
dcAlgoPredictPRFunction to assess the prediction performance via...
dcAlgoPropagateFunction to propagate ontology annotations according to an...
dcAncestralMLFunction to reconstruct ancestral discrete states using fast...
dcAncestralMPFunction to reconstruct ancestral discrete states using...
dcBuildAnnoFunction to build an object of the S4 class Anno from input...
dcBuildInfoDataFrameFunction to build an object of the S4 class InfoDataframe...
dcBuildOntoFunction to build an object of the S4 class Onto from input...
dcConverterFunction to convert an object between graph classes
dcDAGannotateFunction to generate a subgraph of a direct acyclic graph...
dcDAGdomainSimFunction to calculate pair-wise semantic similarity between...
dcDuplicatedFunction to determine the duplicated patterns from input data...
dcEnrichmentFunction to conduct ontology enrichment analysis given a...
dcFunArgsFunction to assign (and evaluate) arguments with default...
dcList2MatrixFunction to convert a list into a matrix containing three...
dcNaivePredictFunction to perform naive prediction from input known...
dcRDataLoaderFunction to load dcGOR built-in RData
dcRWRpipelineFunction to setup a pipeine to estimate RWR-based contact...
dcRWRpredictFunction to perform RWR-based ontology term predictions from...
dcSparseMatrixFunction to create a sparse matrix for an input file with...
dcSplitArchFunction to obtain a list of features via splitting an input...
dcSubtreeCladeFunction to extract a subtree under a given clade from a...
dcSubtreeTipsFunction to extract a tip-induced subtree from a...
dcSupraBetterFunction to find supra-domains with better scores than their...
dcTreeConnectivityFunction to calculate the sparse connectivity matrix between...
Dnetwork-classDefinition for S4 class Dnetwork
Dnetwork-methodMethods defined for S4 class Dnetwork
Eoutput-classDefinition for S4 class Eoutput
Eoutput-methodMethods defined for S4 class Eoutput
eTOLeukaryotic Tree Of Life (eTOL)
Feature2GOBP.interproAnnotations and scores between InterPro domains and Gene...
Feature2GOBP.pfamAnnotations and scores between Pfam domains/combinations and...
Feature2GOBP.sfAnnotations and scores between SCOP domains/combinations (at...
Feature2GOCC.interproAnnotations and scores between InterPro domains and Gene...
Feature2GOCC.pfamAnnotations and scores between Pfam domains/combinations and...
Feature2GOCC.sfAnnotations and scores between SCOP domains/combinations (at...
Feature2GOMF.interproAnnotations and scores between InterPro domains and Gene...
Feature2GOMF.pfamAnnotations and scores between Pfam domains/combinations and...
Feature2GOMF.sfAnnotations and scores between SCOP domains/combinations (at...
Feature2HPPA.interproAnnotations and scores between InterPro domains and Human...
Feature2HPPA.pfamAnnotations and scores between Pfam domains/combinations and...
Feature2HPPA.sfAnnotations and scores between SCOP domains/combinations (at...
InfoDataFrame-classDefinition for S4 class InfoDataFrame
InfoDataFrame-methodMethods defined for S4 class InfoDataFrame
InterProInterPro domains (InterPro).
InterPro2GOBPAnnotations of InterPro domains by Gene Ontology Biological...
InterPro2GOCCAnnotations of InterPro domains by Gene Ontology Cellular...
InterPro2GOMFAnnotations of InterPro domains by Gene Ontology Molecular...
Onto-classDefinition for S4 class Onto
onto.DODisease Ontology (DO).
onto.ECEnzyme Commission (EC).
onto.GOBPGene Ontology Biological Process (GOBP).
onto.GOCCGene Ontology Cellular Component (GOCC).
onto.GOMFGene Ontology Molecular Function (GOMF).
onto.HPMIHuman Phenotype Mode of Inheritance (HPMI).
onto.HPONHuman Phenotype ONset and clinical course (HPON).
onto.HPPAHuman Phenotype Phenotypic Abnormality (HPPA).
onto.KWUniProtKB KeyWords (KW).
Onto-methodMethods defined for S4 class Onto
onto.MPMammalian Phenotype (MP).
onto.UPUniProtKB UniPathway (UP).
PfamPfam domains (Pfam).
Pfam2GOBPAnnotations of Pfam domains by Gene Ontology Biological...
Pfam2GOCCAnnotations of Pfam domains by Gene Ontology Cellular...
Pfam2GOMFAnnotations of Pfam domains by Gene Ontology Molecular...
RfamRNA families (Rfam).
Rfam2GOBPAnnotations of Rfam RNA families by Gene Ontology Biological...
Rfam2GOCCAnnotations of Rfam RNA families by Gene Ontology Cellular...
Rfam2GOMFAnnotations of Rfam RNA families by Gene Ontology Molecular...
SCOP.faSCOP domain families (fa).
SCOP.fa2DOAnnotations of SCOP domain families (fa) by Disease Ontology...
SCOP.fa2ECAnnotations of SCOP domain families (fa) by Enzyme Commission...
SCOP.fa2GOBPAnnotations of SCOP domain families (fa) by Gene Ontology...
SCOP.fa2GOCCAnnotations of SCOP domain families (fa) by Gene Ontology...
SCOP.fa2GOMFAnnotations of SCOP domain families (fa) by Gene Ontology...
SCOP.fa2HPMIAnnotations of SCOP domain families (fa) by Human Phenotype...
SCOP.fa2HPONAnnotations of SCOP domain families (fa) by Human Phenotype...
SCOP.fa2HPPAAnnotations of SCOP domain families (fa) by Human Phenotype...
SCOP.fa2KWAnnotations of SCOP domain families (fa) by UniProtKB...
SCOP.fa2MPAnnotations of SCOP domain families (fa) by Mammalian...
SCOP.fa2UPAnnotations of SCOP domain families (fa) by UniProtKB...
SCOP.sfSCOP domain superfamilies (sf).
SCOP.sf2DOAnnotations of SCOP domain superfamilies (sf) by Disease...
SCOP.sf2ECAnnotations of SCOP domain superfamilies (sf) by Enzyme...
SCOP.sf2GOBPAnnotations of SCOP domain superfamilies (sf) by Gene...
SCOP.sf2GOCCAnnotations of SCOP domain superfamilies (sf) by Gene...
SCOP.sf2GOMFAnnotations of SCOP domain superfamilies (sf) by Gene...
SCOP.sf2HPMIAnnotations of SCOP domain superfamilies (sf) by Human...
SCOP.sf2HPONAnnotations of SCOP domain superfamilies (sf) by Human...
SCOP.sf2HPPAAnnotations of SCOP domain superfamilies (sf) by Human...
SCOP.sf2KWAnnotations of SCOP domain superfamilies (sf) by UniProtKB...
SCOP.sf2MPAnnotations of SCOP domain superfamilies (sf) by Mammalian...
SCOP.sf2UPAnnotations of SCOP domain superfamilies (sf) by UniProtKB...
visEnrichmentFunction to visualise enrichment analysis outputs in the...
hfang-bristol/dcGOR documentation built on May 17, 2019, 3:54 p.m.