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

Fit a dyadic mixed model to pedigree data estimating (co)variance components and genetic parameters

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.

Trait Analysis by aSSociation, Evolution and Linkage

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"

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

quangpy: a python package for quantitative genetics analysis

O objetivo do presente projeto é propor e avaliar o uso da regularização no desempenho de RNAs em modelos de predição genômica (GP). Tal estudo visa melhorar a predição de valores genéticos genômicos (GEBV), evitando o chamado o problema de ‘overfitting’, e estimação de parâmetros genéticos. Para isso, dados simulados e reais serão utilizados.

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

Fast multiplication routine for genotype data and an efficient storage format

Genomic and phenomic prediction of agronomic traits and malt quality in NY Winter Malting Barley

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.

R package for average evolvability measures

Complete reproduction of 'Generation-Updated Orthogonal Epistatic Kernels for Cross-Generation Genomic Prediction' - NOIA encoding, multi-kernel AI-REML, forward simulation, ablation study. 137 tests, 100% coverage.