| 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... |
