shinyGAStool: an open-source user-friendly tool for candidate gene association studies implemented in R-shiny
Please cite the tool using this website repository and the manuscript:
Hoffmann TJ, Miaskowski C, Kober KM. ShinyGAStool: A user-friendly tool for candidate gene association studies. SoftwareX. 2023;21:101274. doi: 10.1016/j.softx.2022.101274.
Periodically, we provide a release of the tool as a stand-alone Windows executable with an installation tool. Please see the releases to download the latest version.
Make sure you download the following files & folders, making sure that the files in the data/ folder are put in a data/ subfolder where the main application R source file is (shinyGeneticsApp.R, located in the src directory on the repository, but download the files to the following directory structure):
- src/shinyGeneticsApp.R
- data/anno_ccds_hg19.txt.gz
- data/anno_gencode_attrs_hg38.txt.gz
- data/anno_gencode_attrs_hg19.txt.gz
- data/anno_gencode_basic_hg19.txt.gz
- data/anno_refFlat_hg19.txt.gz
- data/anno_ccds_hg38.txt.gz
- data/anno_gencode_basic_hg38.txt.gz
- data/anno_refFlat_hg38.txt.gz
You can optionally (recommended) download the demo files from (and recommended to put in a demo/ subfolder where the main application source file is):
- demo/kgp-eur.bed
- demo/kgp-eur.bim
- demo/kgp-eur.fam
- demo/kgp-eur-ldl-pheno.csv
You can install R from:
https://cran.r-project.org/
Or install RStudio for a slightly more polished user interface to R:
https://rstudio.com/products/rstudio/
After launching the newly installed R, from the command prompt, type the following to install necessary dependencies:
install.packages("shiny")
install.packages("shinyFiles")
install.packages("DT")
install.packages("compiler")
install.packages("heatmaply")
install.packages("rio")
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("snpStats")
Navigate to the folder that the shiny app (shinyGeneticsApp.R) is located, and type:
source("shinyGeneticsApp.R")
This should launch the interface. A demo dataset is included in the demo directory.
Note: If you are running the shiny app from within RStudio, make sure to set the working directory: Session -> Set Working Directory -> To Source File Location
Thomas Hoffmann: Thomas.Hoffmann@ucsf.edu
Kord M. Kober: Kord.Kober@ucsf.edu
Support for this project was provided by the National Cancer Institute (CA233774). Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the National Institute of Health.