VarGen

VarGen is an R package that fetches, annotates, and ranks disease-related variants using public databases such as Online Mendelian Inheritance in Man, the Functional Annotation of the Mammalian genome 5, the Genotype-Tissue Expression, and the Genome Wide Association Studies catalog. The package is customizable and capable of identifying the most impactful variants.

Topic

GWAS study;DNA polymorphism;Pathology;Mapping;Genotype and phenotype

Detail

  • Operation: SNP detection;Variant filtering;Data retrieval

  • Software interface: Command-line user interface

  • Language: R

  • License: The MIT licence + file LICENSE

  • Cost: Free

  • Version name: 0.2.1

  • Credit: European Union’s Horizon 2020-funded project Nutrishield

  • Input: -

  • Output: -

  • Contact: f.mohareb@cranfield.ac.uk

  • Collection: -

  • Maturity: -

Publications

  • VarGen: an R package for disease-associated variant discovery and annotation.
  • Molitor C, et al. VarGen: an R package for disease-associated variant discovery and annotation. VarGen: an R package for disease-associated variant discovery and annotation. 2020; 36:2626-2627. doi: 10.1093/bioinformatics/btz930
  • https://doi.org/10.1093/bioinformatics/btz930
  • PMID: 31834354
  • PMC: -

Download and documentation

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