plant-breeding

Repository for version control of the BrAPI specifications

Utilities for field trial analysis.

Code for "Using machine learning to combine genetic and environmental data for maize grain yield predictions across multi-environment trials" (Fernandes et. al 2024)

📈🌱 Mixed Models for Agriculture in R

We present here a 1D convolutional neural network model to predict grain protein content using spectroscopic data of multiple cereals

Using near-infrared spectroscopy (NIRS) and machine learning to determine oleic acid content from peanut raw grains

Envirotyping Library for Quantitative Genetics and Genomics

Tools and Statistical Procedures in Plant Science

Modeling of nutritional traits from multiple crops using NIRS and machine learning/statistics

R package for agricultural statistics — 16 ANOVA designs, 7 post-hoc tests, 7 stability methods. Published on CRAN.

Analysis of Selection Index in Plant Breeding

📉🌱 R für Bio- und Agrarwissenschaftler

Diallel analysis of carrot phenotypes

A collaborative BrAPI v2.1 workspace for multi-agent research via MCP. Search studies, germplasm, genotypes, and more across Breedbase, T3, Sweetpotatobase, and any BrAPI v2-compliant server.

Bulk Segregant Analysis for QTL mapping from pooled whole-genome sequencing data.

Python library for data extraction from drone orthomosaics in plant breeding trials.

Characterise near-isogenic and backcross-derived lines against their parents from SNP genotypes, in the browser. Open source.

Correspondence-free pipeline for validating genomic diversity maps of sweet potato collections. PCA/UMAP + kNN graphs on DArT SNP matrices; PCA-30D vs autoencoders in n≪p regimes. Conference poster.

Local, open-source Primer-BLAST for plant breeding: Primer3 + BLAST+, multi-reference specificity, in-silico PCR, CAPS/dCAPS, offline

Bioinformatic workflow, statistical analysis and figure preparation for the "Wild again: Recovery of a beneficial Cannabis seed endophyte from low domestication genotypes" MS