the hierfstat package
Envirotyping Library for Quantitative Genetics and Genomics
Testing pleiotropy vs. separate QTL in multiparental populations
Diallel analysis of carrot phenotypes
Quantitative and population genetics analyses of populations, pools, half-sib/full-sib families, and polyploids
Genetic evaluation in R: AI-REML variance components, breeding values and single-step genomics (ssGBLUP, APY), with reaction norms, indirect genetic effects, multi-trait, threshold and survival models. The numerics are C++ inside the package, with no run-time dependency.
List of papers related to Agricultural Statistics, Plant Breeding, and Quantitative Genetics
Trait Analysis by aSSociation, Evolution and Linkage
Genomic and phenomic prediction of agronomic traits and malt quality in NY Winter Malting Barley
Fit a dyadic mixed model to pedigree data estimating (co)variance components and genetic parameters
Benchmarking 86 heritability estimation configurations and downstream polygenic risk score performance across UK Biobank phenotypes. Associated paper: arXiv:2604.02394
Comprehensive biometrical and genetic analysis tools for plant breeders, researchers and agricultural scientists. It provides functions for randomized complete block design (rcbd), completely randomized design (crd), genetic variability, analysis of variance (ANOVA), post-hoc tests, multivariate diagnostics PCA and cluster analysis.
quangpy: a python package for quantitative genetics analysis
A field experiment assessing the adaptive capacity of a wild plant population (Brassica rapa) to expected warming
Анализ генетических данных в R с использованием BLUP. Смешанные линейные модели, подготовка данных и оценка генетической ценности
Analysis workflow for optimizing pickling cucumber multi-environment trial networks using environmental covariates, production importance, and future climate projections.
This repository contains data and code to reproduce analysis in the manuscript, "A mutation in Themis contributes to peanut-induced oral anaphylaxis in CC027 mice"
QTL mapping of chicken comb mass with R/qtl, including covariate adjustment, permutation tests, and QTL refinement. Reproducible with Quarto and renv
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