Software
CropGenoViz
An R Shiny app for exploring crop genetic diversity from a genotype × trait data table: data overview and validation, correlation analysis between traits, PCA and hierarchical clustering (via FactoMineR/factoextra), and multi-trait genotype selection using the MGIDI index (via the metan package). Built with R, Shiny, and bslib.
SCIFI: a class-calibrated, cross-trial selection index for sweet corn
An R Shiny companion app for SCIFI (Sweet Corn Ideotype Fitness Index), which consolidates 21 independently run sweet- and specialty-corn breeding trials (927 genotype-records, Vietnam National University of Agriculture, 2018-2024) that share almost no common germplasm, trait list, or selection method into one comparable score. Ten agronomic and quality criteria (yield, Brix, pericarp thickness, ear length and diameter, kernel rows per ear, kernels per row, plant height, ear height, and days to fresh harvest) are each converted to a desirability score and combined by a non-compensatory geometric mean, with boundaries calibrated from pooled cross-trial percentiles. Because parental inbred lines and their own F1 hybrids were found to score systematically differently on heterosis-sensitive traits, the app offers three class-calibrated scoring scales (pooled, hybrid, and parental line) rather than one shared scale. It also lets a user compare SCIFI directly against every selection method this program has used before (MGIDI, MTSI, WAASB, Smith-Hazel index, Smith index) and upload a new trial’s own raw data to run descriptive statistics, ANOVA, and PCA before scoring it. Includes an interactive calculator and a searchable table of 871 real analysis results. Built with R, Shiny, bslib, ggplot2, and DT. Manuscript in preparation.