GenoBrew is a user-friendly R Shiny application for measuring marker panel efficiency according to dataset, help users optmize markers selection, perform basic relationship analysis, and visualization of copy number variation (CNV) profiles. It includes built-in datasets for alfalfa genomic data exploration and analysis, designed to support breeders and researchers without requiring command-line expertise.
- Web-Based Interface: Run analyses directly in the browser — no command-line required.
- Select Markers module: Compare marker statistics derived from whole-genome sequencing (WGS), GBS, or other sequencing technology with a set marker panel.
- CNV Profiles module: Explore interactive visualizations of copy number variation profiles across samples. Also visualize relationship statistics for families.
- Built-in datasets: Includes the Alfalfa F1 population dataset, ready to load for analysis. This dataset is publicly available and validated using the Alfalfa 3k DArTag marker panel.
- Upload your own data: Accepts VCF and CNV files in CSV/TSV/GZ formats alongside a custom marker panel CSV.
Loads a VCF file (or built-in WGS dataset) and a marker panel, then computes and displays:
- WGS marker count, panel marker count, common markers, and markers passing filters
- Interactive marker distribution plot
- Filters: minimum MAF, maximum missing data, depth range, heterozygosity range, maximum % CNV ≠ 2
- Genomic relationship plots
Loads a CNV file (or built-in dataset) and visualizes:
- Genome-wide CNV profiles for combined samples
- BAF, zscore and CNV calls plots for single sample
- Pairwise IBD plots
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Install R (≥ 4.1.0) from CRAN.
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Install GenoBrew:
if (!require("remotes", quietly = TRUE)) install.packages("remotes")
remotes::install_github("Breeding-Insight/GenoBrew", dependencies = TRUE)- Launch the app:
GenoBrew::run_app()- The GenoBrew interface will open in your default web browser.
GenoBrew development is supported by Breeding Insight, a USDA-funded initiative hosted at the University of Florida – IFAS.
This project is licensed under the Apache-2.0 license. See LICENSE for details.