SCOP domain superfamilies (sf).
Methods defined for S4 class Eoutput
Function to propagate ontology annotations according to an input file
Function to determine the duplicated patterns from input data matrix
Function to conduct ontology enrichment analysis given a group of domains
Annotations of InterPro domains by Gene Ontology Cellular Component (GOCC).
Annotations of Rfam RNA families by Gene Ontology Cellular Component (GOCC).
Annotations of InterPro domains by Gene Ontology Molecular Function (GOMF).
Annotations of Pfam domains by Gene Ontology Cellular Component (GOCC).
Function to reconstruct ancestral discrete states using maximum parsimony algorithm
Annotations of SCOP domain superfamilies (sf) by Human Phenotype Phenotypic Abnormality (HPPA).
Function to assign (and evaluate) arguments with default values for an input function
Annotations of SCOP domain superfamilies (sf) by Mammalian Phenotype (MP).
Function to perform RWR-based ontology term predictions from input known annotations and an input graph
Function to extract a tip-induced subtree from a phylo-formatted phylogenetic tree
Gene Ontology Cellular Component (GOCC).
Function to calculate the sparse connectivity matrix between parents and children from a phylo-formatted phylogenetic tree
Annotations of SCOP domain families (fa) by Human Phenotype Phenotypic Abnormality (HPPA).
Gene Ontology Molecular Function (GOMF).
Function to predict ontology terms given domain architectures (including individual domains)
Function to predict ontology terms for genomes with domain architectures (including individual domains)
Annotations of SCOP domain families (fa) by Human Phenotype Mode of Inheritance (HPMI).
Annotations of Rfam RNA families by Gene Ontology Biological Process (GOBP).
Function to build an object of the S4 class InfoDataframe from an input file
InterPro domains (InterPro).
Methods defined for S4 class Onto
Definition for S4 class Coutput
Methods defined for S4 class Dnetwork
Definition for S4 class Anno
Methods defined for S4 class Cnetwork
Annotations of SCOP domain superfamilies (sf) by Gene Ontology Cellular Component (GOCC).
Annotations of SCOP domain families (fa) by Gene Ontology Molecular Function (GOMF).
Definition for S4 class Eoutput
Function to calculate pair-wise semantic similarity between domains based on a direct acyclic graph (DAG) with annotated data
Annotations of SCOP domain families (fa) by Gene Ontology Biological Process (GOBP).
Function to load dcGOR built-in RData
Function to apply dcGO algorithm to infer domain-centric ontology
Definition for VIRTUAL S4 class AdjData
Annotations of SCOP domain superfamilies (sf) by Human Phenotype ONset and clinical course (HPON).
Annotations of SCOP domain superfamilies (sf) by Gene Ontology Biological Process (GOBP).
Human Phenotype Mode of Inheritance (HPMI).
Definition for S4 class Cnetwork
Function to setup a pipeine to estimate RWR-based contact strength between samples from an input domain-sample data matrix and an input graph
Function to convert a list into a matrix containing three columns
Mammalian Phenotype (MP).
Definition for S4 class Dnetwork
Methods defined for S4 class Coutput
Function to build an object of the S4 class Anno from input files
Disease Ontology (DO).
Annotations of SCOP domain superfamilies (sf) by Human Phenotype Mode of Inheritance (HPMI).
Function to find supra-domains with better scores than their individual domains
eukaryotic Tree Of Life (eTOL)
Function to extract a subtree under a given clade from a phylo-formatted phylogenetic tree
Annotations of Pfam domains by Gene Ontology Biological Process (GOBP).
Function to create a sparse matrix for an input file with three columns
Function to predict ontology terms given an input file containing domain architectures (including individual domains)
Definition for S4 class InfoDataFrame
Ancestral superfamily domain repertoires in Eukaryotes
Annotations of SCOP domain families (fa) by Human Phenotype ONset and clinical course (HPON).
Definition for VIRTUAL S4 class AnnoData
Function to obtain a list of features via splitting an input architecture
Function to convert an object between graph classes
Annotations of SCOP domain families (fa) by Gene Ontology Cellular Component (GOCC).
RNA families (Rfam).
Annotations of SCOP domain superfamilies (sf) by Gene Ontology Molecular Function (GOMF).
Annotations of Pfam domains by Gene Ontology Molecular Function (GOMF).
Annotations of Rfam RNA families by Gene Ontology Molecular Function (GOMF).
Methods defined for S4 class Anno
SCOP domain families (fa).
Human Phenotype Phenotypic Abnormality (HPPA).
Annotations of SCOP domain superfamilies (sf) by Disease Ontology (DO).
Methods defined for S4 class InfoDataFrame
Function to generate a subgraph of a direct acyclic graph (DAG) induced by the input annotation data
Function to reconstruct ancestral discrete states using fast maximum likelihood algorithm
Function to perform naive prediction from input known annotations
Pfam domains (Pfam).
Human Phenotype ONset and clinical course (HPON).
Annotations of SCOP domain families (fa) by Disease Ontology (DO).
Gene Ontology Biological Process (GOBP).
Function to assess the prediction performance via Precision-Recall (PR) analysis
Annotations of InterPro domains by Gene Ontology Biological Process (GOBP).
Function to visualise enrichment analysis outputs in the context of the ontology hierarchy
Annotations of SCOP domain families (fa) by Mammalian Phenotype (MP).
Function to build an object of the S4 class Onto from input files
Definition for S4 class Onto