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Codebase for MSc Thesis, Improving Genetic Association for Insect Resistance Traits in Plants Using Deep Learning on Video Tracking Data. Statistics & Data Science at Leiden University

Jupyter Notebook 12.29% Python 77.67% R 10.03%

improving-genetic-association-using-deep-learning_demo's Introduction

Thesis project: Improving genetic association using deep learning

Raw data is available in a private Kaggle repository. Access may be requested.

All results are available here.

Reproducibility usage:

All representations (traits) generated through Deep Learning algorithms can be extracted by running 'run_deep_models.py'. It will download the raw data and do all the cleaning processes and feature engineering. Then it will fit all the models and extract the representations.
With the representations: GWAS, heritability and other statistics used can be replicated by runing 'GWAS_R2_H2.R' in src/model/.
Reverse GWAS can be run with 'Reverse_GWAS.py' in src/model/.
With representations and statistics: All generated images can be replicated using 'Plot_maker.ipynb' and 'Plot_maker.Rmd'.

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