🚴 Kinship Adjusted Multi-Loci Best Linear Unbiased Prediction

R front-end for TASSEL

Can deep learning improve genomic prediction of complex human traits? by Pau Bellot, Gustavo de los Campos, Miguel Pérez-Enciso, Genetics

2024 BreedWheat Genomic Selection pipeline

Trait BLUP, a Feature Selection Package for Genomic Prediction

scripts and examples

Using machine learning to integrate genetic and environmental data to model genotype-by-environment interactions

Training set determination for genomic selection.

Genomic prediction of amino acid traits in Arabidopsis seeds

Solves kernel ridge regression within the the mixed model framework. All the estimated components and parameters, e.g. BLUP of dual variables and BLUP of random predictor effects for the linear kernel (also known as RR-BLUP), are available.

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

This project documents informatics and genomic prediction to support the National Root Crop Research Institute 2021 cassava genomic selection breeding program.

Role of genomics on regulating rice grain metabolic variability under warmer nights: A statistical and image-based deep learning approach

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

Some deep learning genomics projects

Evaluating metabolic and genomic data for predicting grain traits under high night temperature stress in rice

BAMdelbee is a novel tool for discovering homozygous deletions in Whole-exome-sequencing (WES) and whole-genome-sequencing (WGS) data. WES or WGS samples generated by the same method produce BAM files with similar alignment coverage across the genome. BAMdelbee locates homozygous deletions by pinpointing regions covered in all samples but the on…

Gradient Boosting Regression (GBR, https://github.com/scikit-learn/scikit-learn) model for genomic predictions

TARI 2020 GS: (1) Conversion of DArTseqLD data and imputation of DArT report DCas20-5629 (with GS C1). (2) Cross-validation and genomic prediction

Impact of LD regional heterogeneity on genome prediction and heritability estimation in livestock