Welcome to the GenomicPrediction_DataBootcamp repository! This repository contains resources, code examples, and hands-on activities for the Data Bootcamp for Genomic Prediction in Plant Breeding I attended on June 2023. This bootcamp was designed to provide you with a comprehensive understanding of common data structures, analysis techniques, and tools used for genomic selection in plant breeding. The instructor for the boot camp was Prof. Aaron Lorenz from the University of Minnesota.
The GenomicPrediction_DataBootcamp was an intensive course that covered a wide range of topics related to genomic prediction in plant breeding. Through a combination of lectures and hands-on activities, you will gain practical experience and knowledge in the following areas:
- Formatting and quality control of genotype/phenotype data for genomic prediction.
- Implementation and exploration of various types of models for genomic prediction.
- Techniques in cross-validation for assessing prediction accuracy.
- Optimization of training populations for improved prediction performance.
- Multi-trait prediction for simultaneous prediction of multiple traits.
- Genomic prediction for genotype-by-environment interactions (GxE).
- Predictions of all possible crosses (genomic mating) using genomic prediction.
- Exploring other special topics in genomic prediction.
- Tour of available tools for implementing genomic prediction.
This repository is organized into the following sections:
- Lectures: Here, you will find hands-on activities and exercises to further reinforce your understanding of genomic prediction methods. These activities will allow you to practice applying the techniques covered in the bootcamp to solve specific problems and analyze genomic data.
- Scripts: In this directory, you will find practical code examples and scripts that demonstrate the implementation of different genomic prediction models and techniques. These examples are designed to help you apply the concepts learned in the lectures to real-world datasets.
- Slides: This directory contains lecture materials and slide decks covering various topics related to genomic prediction in plant breeding.
- Literature: This directory contains additional resources, such as relevant papers, documentation, and reference materials that can complement your learning journey. Feel free to explore these resources for further study and deeper understanding of genomic prediction in plant breeding.
If you have any suggestions, improvements, or additional resources that you believe would benefit this bootcamp, feel free to contribute to this repository. Please create a pull request with your proposed changes, and our team will review it accordingly.
We hope you find this GenomicPrediction_DataBootcamp repository helpful and that it enhances your understanding of genomic prediction techniques in plant breeding.
For any questions or concerns, please don't hesitate to reach out to me.
Best regards,
Luis Fernando Delgado Munoz
Data Analyst CIAT Cassava programm