An open-source R package for analysing domain-centric ontologies and annotations (dcGO and others)

Features

• Database: R package providing domain-centric annotations by organism-independent ontologies (eg “Gene Ontology”) and organism-specific ontologies (eg “Human Phenotype” and “Mammalian Phenotype”). Entities can be domains taken from SCOP (at both the superfamily and family levels), Pfam and InterPro, and also can be domain-like features (eg Rfam RNA families). See Documentations
• Infrastructure: data structure storing domains (as objects of S4 class InfoDataFrame), annotations (as objects of S4 class Anno), ontologies (as objects of S4 class Onto), enrichment outputs (as objects of S4 class Eoutput), domain networks (as objects of S4 class Dnetwork), and RWR-based contact network outputs (as objects of S4 classes Cnetwork and Coutput)
• True-path rule: able to propagate annotations to all ancestor terms. See dcDAGannotate
• Enrichment analysis: domain-based enrichment analysis and visualisation. See dcEnrichment and visEnrichment
• Semantic similarity: semantic similarity between pairs of domains according to their annotations by an ontology, resulting in a domain (semantic similarity) network. See dcDAGdomainSim
• Random Walk with Restart: support for walk on a domain network to estimate contact (statistically significance) network. See dcRWRpipeline
• Parallel computing: most of analyses are supported with parallel option to reduce runtime
• Customisation: user-input data used to build objects for domains (see dcBuildInfoDataFrame), annotations (see dcBuildAnno) and ontologies (see dcBuildOnto). Also supported for these customised objects are analyses such as dcEnrichment (also visEnrichment) and dcDAGdomainSim

New Functionalities

• dcGO Algorithm: functions used for creating domain-centric ontology. See dcAlgo and dcAlgoPropagate
• dcGO Predictor: functions and databases used for predicting ontology terms from input protein domain contents. See dcAlgoPredictMain (also dcAlgoPredict) and dcAlgoPredictPR, and dcAlgoPredictGenome
• Ancestral reconstruction: functions and databases used for reconstructing ancestral states for discrete characters (eg domain architectures across tree of life). See dcAncestralMP and dcAncestralML