Breedverse is a modular R Shiny application developed by Breeding Insight at University of Florida (UF/IFAS). It serves as a unified hub that lets users install and launch specialized breeding analysis tools — all from a single interface, with no command-line setup required.
Breedverse itself is a lightweight launcher. After installing it, users can install any combination of analysis modules directly from within the app. Each module unlocks a dedicated section in the sidebar with its own set of analysis tools.
Install Breedverse from GitHub using remotes:
# install.packages("remotes")
remotes::install_github("Breeding-Insight/Breedverse")Then launch the app:
Breedverse::run_app()Modules are installed from within the app via the Install Modules page. Each module is sourced from GitHub and loaded dynamically. A restart of the app is required after installation to activate the new features.
GitHub:
Cristianetaniguti/Qploidy
| Feature | Description |
|---|---|
| Standardization | Allele intensities / read counts standardization |
| Ploidy Estimation | Sample-level ploidy inference |
| Aneuploidy Detection | Identify chromosomal copy-number aberrations |
GitHub:
Breeding-Insight/BIGapp
| Category | Feature |
|---|---|
| Genotype Processing | Convert dosage files to VCF |
| Dosage Calling | Off-target SNP calling with updog |
| Filtering | VCF quality filtering |
| Summary Metrics | Genomic diversity statistics |
| Population Structure | PCA, DAPC |
| GWAS | Genome-Wide Association Studies |
| Genomic Selection | GS model fitting and prediction |
GitHub:
Breeding-Insight/familia
| Mode | Feature |
|---|---|
| Unsupervised | SNMF — ADMIXTURE-like ancestry proportions |
| Supervised | PolyBreedTools — reference-panel-based ancestry assignment |
| Ploidy Support | Compatible with diploid and polyploid species |
GitHub:
Breeding-Insight/AlloMate
| Feature | Description |
|---|---|
| Relatedness | Evaluate genetic relatedness among breeding candidates |
| Multi-trait Index | Combine EBVs across traits using user-defined weights |
| OCS | Optimum Contribution Selection to maximize genetic gain |
| Mating Plans | Generate feasible mating lists under kinship constraints |
GitHub:
Breeding-Insight/GenoBrew
| Feature | Description |
|---|---|
| Marker Panel Tests | Test marker panel performance with historical data |
| Interactive filters | Markers basic filters |
| CNV profiles | Interactive visualization of Qploidy2 CNV profiles results |
| CNV hotspots | Find copy number variation hostspots in the genome |
- R ≥ 3.6.0
- Internet connection for module installation (modules are pulled from GitHub)
- Website: https://www.breedinginsight.org
- Contact: https://breedinginsight.org/contact-us/