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dcGOR
View on CRAN: Click
here
Download and install dcGOR package within the R console
Install from CRAN:
install.packages("dcGOR")
Install from Github:
library("remotes")
install_github("cran/dcGOR")
Install by package version:
library("remotes")
install_version("dcGOR", "1.0.6")
Attach the package and use:
library("dcGOR")
Maintained by
Hai Fang
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2014-07-02
Latest Update: 2023-08-18
Description:
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.
How to cite:
Hai Fang (2014). dcGOR: Analysis of Ontologies and Protein Domain Annotations. R package version 1.0.6, https://cran.r-project.org/web/packages/dcGOR. Accessed 21 Nov. 2024.
Previous versions and publish date:
Other packages that cited dcGOR R package
View dcGOR citation profile
Other R packages that dcGOR depends,
imports, suggests or enhances
Functions, R codes and Examples using
the dcGOR R package
Some associated functions: AdjData-class . Ancestral_domainome . Anno-class . Anno-method . AnnoData-class . Cnetwork-class . Cnetwork-method . Coutput-class . Coutput-method . Dnetwork-class . Dnetwork-method . Eoutput-class . Eoutput-method . InfoDataFrame-class . InfoDataFrame-method . InterPro . InterPro2GOBP . InterPro2GOCC . InterPro2GOMF . Onto-class . Onto-method . Pfam . Pfam2GOBP . Pfam2GOCC . Pfam2GOMF . Rfam . Rfam2GOBP . Rfam2GOCC . Rfam2GOMF . SCOP.fa . SCOP.fa2DO . SCOP.fa2GOBP . SCOP.fa2GOCC . SCOP.fa2GOMF . SCOP.fa2HPMI . SCOP.fa2HPON . SCOP.fa2HPPA . SCOP.fa2MP . SCOP.sf . SCOP.sf2DO . SCOP.sf2GOBP . SCOP.sf2GOCC . SCOP.sf2GOMF . SCOP.sf2HPMI . SCOP.sf2HPON . SCOP.sf2HPPA . SCOP.sf2MP . dcAlgo . dcAlgoPredict . dcAlgoPredictGenome . dcAlgoPredictMain . dcAlgoPredictPR . dcAlgoPropagate . dcAncestralML . dcAncestralMP . dcBuildAnno . dcBuildInfoDataFrame . dcBuildOnto . dcConverter . dcDAGannotate . dcDAGdomainSim . dcDuplicated . dcEnrichment . dcFunArgs . dcList2Matrix . dcNaivePredict . dcRDataLoader . dcRWRpipeline . dcRWRpredict . dcSparseMatrix . dcSplitArch . dcSubtreeClade . dcSubtreeTips . dcSupraBetter . dcTreeConnectivity . eTOL . onto.DO . onto.GOBP . onto.GOCC . onto.GOMF . onto.HPMI . onto.HPON . onto.HPPA . onto.MP . visEnrichment .
Some associated R codes: Full dcGOR package functions and examples
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