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 16 Jul. 2026.
Previous versions and publish date:
(2026-07-09 08:29), 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

schoolmath  
Functions and Datasets for Math Used in School
Contains functions and datasets for math taught in school. A main focus is set to prime-calculation. ...
Download / Learn more Package Citations See dependency  
stevedata  
Steve's Toy Data for Teaching About a Variety of Methodological, Social, and Political Topics
This is a collection of various kinds of data with broad uses for teaching. My students, and academ ...
Download / Learn more Package Citations See dependency  
tibble  
Simple Data Frames
Provides a 'tbl_df' class (the 'tibble') with stricter checking and better formatting than the tradi ...
Download / Learn more Package Citations See dependency  
Rnmr1D  
Perform the Complete Processing of a Set of Proton Nuclear Magnetic Resonance Spectra
Perform the complete processing of a set of proton nuclear magnetic resonance spectra from the free ...
Download / Learn more Package Citations See dependency  
tarchetypes  
Archetypes for Targets
Function-oriented Make-like declarative pipelines for Statistics and data science are supported in t ...
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  

27,806

R Packages

239,283

Dependencies

73,837

Author Associations

27,807

Publication Badges

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