quantitative-genetics

the hierfstat package

Testing pleiotropy vs. separate QTL in multiparental populations

Quantitative and population genetics analyses of populations, pools, half-sib/full-sib families, and polyploids

Diallel analysis of carrot phenotypes

List of papers related to Agricultural Statistics, Plant Breeding, and Quantitative Genetics

My Code Collection

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

Trait Analysis by aSSociation, Evolution and Linkage

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.

Анализ генетических данных в R с использованием BLUP. Смешанные линейные модели, подготовка данных и оценка генетической ценности

A field experiment assessing the adaptive capacity of a wild plant population (Brassica rapa) to expected warming

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"

quangpy: a python package for quantitative genetics analysis

Version controlled, editable source for the genetic group 'How To': Wolak & Reid (2017) Journal of Animal Ecology, Appendix S6

Supplementary code and data for "The paradox of predictability"

Genetic mapping and QTL analysis across F₂ to F₆ populations to identify genomic regions controlling target traits using R and ICIMapping.

Code and analysis pipeline for the paper "Genomic Prediction through Machine Learning and Neural Networks for Traits with Epistasis" (Comput Struct Biotechnol J, 2022).

Plant-breeding analytics: mixed-model BLUPs, genomic prediction, combining ability & cross planning — with a grounded assistant that explains results only from verified computation. TypeScript orchestrator + R compute kernel.