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Background: Population structure and ancestry inference are routine in human genetics, yet remain inconvenient for non-experts because canonical tools (PLINK, GCTA, ADMIXTURE) require command-line expertise and careful data management. Results: BPGA (Basic Population Genetic Analysis) is an open‑source R/Shiny application that provides an interactive workflow for educational and exploratory population genetic analyses on datasets in PLINK binary format. BPGA executes LD‑pruned PCA, genome‑wide Fst scans, and ADMIXTURE clustering from a guided interface, and it can optionally merge user data with curated worldwide reference panels (1000 Genomes Project and Human Genome Diversity Project). The app produces publication‑ready figures (PNG/HTML), interactive views (plotly/leaflet), and preserves logs for reproducibility. Availability: Source code is available at https://github.com/jfibla/BPGA-a-Shiny-app-to-perform-Basic-Population-Genetic-Analysis under the Apache‑2.0 license. Conclusions: BPGA lowers the barrier between raw genotype data and interpretable population‑genetic summaries for research and teaching, while keeping analyses transparent and reproducible.
https://doi.org/10.32942/X2VC7T
Bioinformatics, Education, Genetics and Genomics, Higher Education, Life Sciences
Population genetics, PCA, admixture, FST, Human Genetics, methods/software, genomics
Published: 2025-08-31 14:18
Last Updated: 2026-01-09 12:19
CC BY Attribution 4.0 International
Conflict of interest statement:
The author declares no competing interests
Data and Code Availability Statement:
Source code is openly available at https://github.com/jfibla/BPGA-a-Shiny-app-to-perform-Basic-Population-Genetic-Analysis. A hosted demo is also available at http://15.188.54.171:3838/bpga_app/
Language:
English
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