Github repository for the paper "Haplotype-based Autoencoders Can Reduce the Dataset Dimension and Estimate Haplotype Block Effects" which will provide code and examples of how to implement an autoencoder for dimensionality reduction and estimating haplotype bock effects.
Datasets contains the previously unpublished wheat and oat data used in this paper.
The standalone example provided here is based on the data from Technow et al. (2014). Supplementary Tables 1-3 contain genetic data, phenotypes and a map.