Currently, Breeding Insight provides bioinformatic processing support for our external collaborators. This R shiny app will a provide web-based user friendly way for our internal and external collaborators to analyze genomic data without needing to use command-line tools.
Initial supported analyses will include the mature genomics/bioinformatics pipelines developed within Breeding Insight, with additional analyses continuing to be added.
Supported:
- Dosage calling from MADC file
- SNP filtering
- Population Structure
- PCA
- DAPC
- Genomic Diversity
- GWAS
In-progress:
- Genomic Prediction/Selection
Local computer
- Install R
- Download this folder from GitHub
- Open Terminal (mac)
- Initialize R in Terminal and enter the below commands
install.packages("shiny") #This is only needed for the first time running shiny
library("shiny") #Starting the shiny package
setwd("path_to_shiny_app/Genomics_Shiny_App") #Direct R to the downloaded app folder
runApp("BIG_app") #Start the app
- View shiny app in browser
Online (in progress)
The BIG app relies on both custom scripts and previously developed R packages cited below:
required_cran_packages <- c("updog", "ggplot2","devtools","GWASpoly","SNPRelate", "adegenet", "future", "scales", "AGHmatrix", "stats", "factoextra", "readxl", "ggrepel", "dplyr", "shiny", "shinydashboard","randomcoloR","plotly", "DT","RColorBrewer", "dichromat", "bs4Dash", "shinyWidgets","data.table", "matrixcalc","Matrix", "shinyalert","rrBLUP", "tidyverse", "foreach", "doParallel","VariantAnnotation", "vcfR")
required_bio_packages <- c("SNPRelate","VariantAnnotation")
Dev_tools_packages <- c("GWASpoly")
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
Breeding Insight is funded by USDA through Cornell University.