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alex-sandercock authored Dec 22, 2024
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# (B)reeding (I)nsight (G)enomics app <img src="https://github.com/user-attachments/assets/136c5ec4-5093-4129-a41b-233945e54198" align="right" width="250"/>

Currently, Breeding Insight provides bioinformatic processing support for our external collaborators. This R shiny app will provide a web-based user friendly way for our internal and external collaborators to analyze genomic data without needing to use command-line tools.
The BIGapp is a user-friendly tool for processing low to mid-density genotyping data for diploid and polyploid species. This R shiny app provides a web-based user friendly way for users to analyze genomic data without needing to use command-line tools. Additional analysis will be added, with the initial focus on a core set of features for supporting breeding decisions.

### Supported Analyses

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- SNP filtering
- Sample filtering
- Summary metrics
- SNP Allele Frequency
- SNP Polymorphism Information Content
- SNP Minor Allele Frequency
- Sample Observed Heterozygosity
- Population Structure
- PCA
- DAPC
- GWAS
- GWASpoly
- GS
- Estimate Model Prediction Accuracy
- Predict Trait Values for New Genotypes
- Predict Phenotype Values and EBVs for Samples

### Running the BIG app

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