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dcGOR  

Analysis of Ontologies and Protein Domain Annotations
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]
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:
1.0.0 (2014-07-02 17:08), 1.0.2 (2014-07-25 18:42), 1.0.3 (2014-09-25 13:41), 1.0.4 (2014-12-04 00:23), 1.0.5 (2015-07-20 19:19), 1.0.6 (2015-07-27 10:52)
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