Other packages > Find by keyword >

VarfromPDB  

Disease-Gene-Variant Relations Mining from the Public Databases and Literature
View on CRAN: Click here


Download and install VarfromPDB package within the R console
Install from CRAN:
install.packages("VarfromPDB")

Install from Github:
library("remotes")
install_github("cran/VarfromPDB")

Install by package version:
library("remotes")
install_version("VarfromPDB", "2.2.10")



Attach the package and use:
library("VarfromPDB")
Maintained by
Zongfu Cao
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2015-12-21
Latest Update:
Description:
Captures and compiles the genes and variants related to a disease, a phenotype or a clinical feature from the public databases including HPO (Human Phenotype Ontology, ), Orphanet , OMIM (Online Mendelian Inheritance in Man, ), ClinVar , and UniProt (Universal Protein Resource, ) and PubMed abstracts. 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. Additionally, PubMed provides the primary and latest source of the information. Text mining was employed to capture the information from PubMed abstracts.
How to cite:
Zongfu Cao (2015). VarfromPDB: Disease-Gene-Variant Relations Mining from the Public Databases and Literature. R package version 2.2.10, https://cran.r-project.org/web/packages/VarfromPDB. Accessed 04 Jun. 2026.
Previous versions and publish date:
1.1.0 (2015-12-21 08:54), 2.0.5 (2016-02-11 08:27), 2.1.9 (2016-08-20 16:39), 2.1.10 (2016-10-25 10:39), 2.1.11 (2016-10-31 08:10), 2.2.6 (2017-04-26 07:26), 2.2.7 (2017-05-06 07:19), 2.2.10 (2018-09-13 09:30)
Other packages that cited VarfromPDB R package
View VarfromPDB citation profile
Other R packages that VarfromPDB depends, imports, suggests or enhances
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

crplyr  
A 'dplyr' Interface for Crunch
In order to facilitate analysis of datasets hosted on the Crunch data platform ...
Download / Learn more Package Citations See dependency  
AMPLE  
Shiny Apps to Support Capacity Building on Harvest Control Rules
Three Shiny apps are provided that introduce Harvest Control Rules (HCR) for fisheries management. ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
shinybusy  
Busy Indicators and Notifications for 'Shiny' Applications
Add indicators (spinner, progress bar, gif) in your 'shiny' applications to show the user that the ...
Download / Learn more Package Citations See dependency  
murphydiagram  
Murphy Diagrams for Forecast Comparisons
Data and code for the paper by Ehm, Gneiting, Jordan and Krueger ('Of Quantiles and Expectiles: Con ...
Download / Learn more Package Citations See dependency  
phers  
Calculate Phenotype Risk Scores
Use phenotype risk scores based on linked clinical and genetic data to study Mendelian disease and ...
Download / Learn more Package Citations See dependency  

27,268

R Packages

233,548

Dependencies

72,590

Author Associations

27,205

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA