dcGOR: Analysis of ontologies and protein domain annotations

The package is used to analyse 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 under-development 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; 3) to reconstruct ancestral discrete characters using maximum likelihood/parsimony.

Version: 1.0.4
Depends: R (≥ 3.1.0), Matrix, igraph, dnet
Imports: methods
Suggests: foreach, doMC, ape
Published: 2014-12-04
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang <hfang at cs.bris.ac.uk>
License: GPL-2
URL: http://supfam.org/dcGOR, http://dcgor.r-forge.r-project.org, http://cran.r-project.org/package=dcGOR, https://github.com/hfang-bristol/dcGOR
NeedsCompilation: no
Citation: NA
Materials: NA
CRAN checks: dcGOR results

Downloads:

Reference manual: dcGOR.pdf
Package source: dcGOR_1.0.4.tar.gz
Windows binaries: r-devel: dcGOR_1.0.4.zip, r-release: dcGOR_1.0.4.zip, r-oldrel: not available
OS X Snow Leopard binaries: r-release: dcGOR_1.0.4.tgz, r-oldrel: not available
OS X Mavericks binaries: r-release: dcGOR_1.0.4.tgz
Old sources: dcGOR archive