argyle

Argyle is an R package for analyzing genotyping microarray data, particularly those from Illumina arrays. The package aims to provide a user-friendly interface for non-expert users to perform quality control, normalization, and exploratory analyses of genotyping data. It includes a range of functions for quality checks, data normalization, and visual and statistical summaries. Additionally, argyle offers format-conversion tools to ensure compatibility with popular genetic analysis software such as PLINK, R/qtl, and DOQTL. The package is accompanied by detailed vignettes demonstrating common use cases, making it accessible to many users. By bridging the gap between low-level quality control tasks and high-level genetic analyses, argyle streamlines the workflow for analyzing genotyping microarray data.

Topic

Genotyping experiment;Sequencing;Sequence analysis

Detail

  • Operation: Genotyping

  • Software interface: Command-line interface

  • Language: R

  • License: CC BY-NC-SA 4.0

  • Cost: Free of charge with restrictions

  • Version name: v0.2.0

  • Credit: NIH, the UNC Bioinformatics and Computational Biology Training Grant.

  • Input: -

  • Output: -

  • Contact: Andrew P. Morgan apm@email.unc.edu

  • Collection: -

  • Maturity: -

Publications

  • argyle: An R Package for Analysis of Illumina Genotyping Arrays.
  • Morgan AP. argyle: An R Package for Analysis of Illumina Genotyping Arrays. argyle: An R Package for Analysis of Illumina Genotyping Arrays. 2015; 6:281-6. doi: 10.1534/g3.115.023739
  • https://doi.org/10.1534/g3.115.023739
  • PMID: 26684930
  • PMC: PMC4751548

Download and documentation

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