BIGapp

R
Shiny
GWAS
Genomic Selection
PCA
Polyploid
A user-friendly R Shiny app to analyze genomic data without command-line tools, supporting diploid and polyploid species

A user-friendly R Shiny app to analyze genomic data without command-line tools, supporting diploid and polyploid species

Overview

BIGapp (Breeding Insight Genomics app) is a web application built with R and Shiny that simplifies the processing of low to mid-density genotyping data for both diploid and polyploid species. It provides an intuitive interface for researchers and breeders to analyze genomic data without requiring command-line expertise.

Key Features

  • Web-Based Interface — Access through your browser, no command-line needed
  • Genotype Processing — Call genotypes from read counts, filter SNPs and samples
  • Summary Statistics — SNP PIC, MAF, observed heterozygosity
  • Population Structure — PCA and DAPC analysis
  • GWAS — Genome-wide association studies via GWASpoly
  • Genomic Selection — Model accuracy estimation, predict breeding values
  • Multi-ploidy Support — Works with diploid and polyploid species

Installation

BiocManager::install("Breeding-Insight/BIGapp", dependencies = TRUE)
BIGapp::run_app()

Citation

Sandercock A.M., Peel M.D., Tanigut C.H., et al. (2025). BIGapp: A User-Friendly Genomic Tool Kit Identified Quantitative Trait Loci for Creeping Rootedness in Alfalfa. The Plant Genome. DOI: 10.1002/tpg2.70067

Funding

BIGapp development is supported by Breeding Insight, a USDA-funded initiative.