VarfromPDB: Capture the Genes and Variants Related to a Genetic Disease from Public Databases

Captures and compiles the genes and variants related to a disease, a phenotype or a clinical feature based on the public databases including HPO (Human Phenotype Ontology, http://human-phenotype-ontology.github.io/about.html), Orphanet (http://www.orpha.net/consor/cgi-bin/index.php), OMIM (Online Mendelian Inheritance in Man, http://www.omim.org), ClinVar (http://www.ncbi.nlm.nih.gov/clinvar), and Uniprot (Universal Protein Resource, http://www.uniprot.org). HPO provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. HPO currently contains approximately 11,000 terms and over 115,000 annotations to hereditary diseases. Orphanet is the reference portal for information on rare diseases and orphan drugs, whose aim is to help improve the diagnosis, care and treatment of patients with rare diseases. OMIM is a continuously updated catalog of human genes and genetic disorders and traits, with particular focus on the molecular relationship between genetic variation and phenotypic expression. ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. Uniprot focuses on amino acid altering variants imported from Ensembl Variation databases. For Homo sapiens, the variants including human polymorphisms and disease mutations in the Uniprot are manually curated from UniProtKB/Swiss-Prot.

Version: 1.1.0
Depends: R (≥ 3.0.0), stringr, XML, XML2R, RCurl
Published: 2015-12-21
Author: Zongfu Cao
Maintainer: Zongfu Cao <caozongfu at gmail.com>
License: GPL-2
NeedsCompilation: no
CRAN checks: VarfromPDB results

Downloads:

Reference manual: VarfromPDB.pdf
Package source: VarfromPDB_1.1.0.tar.gz
Windows binaries: r-devel: VarfromPDB_1.1.0.zip, r-release: VarfromPDB_1.1.0.zip, r-oldrel: VarfromPDB_1.1.0.zip
OS X Snow Leopard binaries: r-release: VarfromPDB_1.1.0.tgz, r-oldrel: not available
OS X Mavericks binaries: r-release: VarfromPDB_1.1.0.tgz