Phylogenetic augmentation paper analysis

This repository has all the code necessary for reproducing the results from the paper titled Improving the performance of supervised deep learning for regulatory genomics using phylogenetic augmentation by Andrew G Duncan, Jennifer A Mitchell, and Alan M Moses.

Start here

To recreate the results from the analysis, follow the steps below.

Download input data

Download all of the data from Zenodo at https://zenodo.org/records/10463493

See ./input/README.md

Setup the environment and run analysis

The analyses must be run from the ./phylogenetic_augmentations directory.

See ./phylogenetic_augmentations/README.md

View results

The results from running the analysis are found in ./output and ./figures.