Jonathan-Mandl/ExoShorkie-models

ExoShorkie – Trained Models

This repository contains trained ExoShorkie and NatShorkie models used in:

ExoShorkie: Predicting RNA-seq coverage of exogenous genomes in yeast by transfer learning

Contents

The Models/ directory includes fine-tuned models for each genome:

• Models/Human_chr_7 – Human chromosome 7
• Models/Data_storage_chr – Artificial data-storage chromosome
• Models/HPRT1 – HPRT1 genomic construct
• Models/HPRT1R – Reversed HPRT1 construct
• Models/M_mycoides – Mycoplasma mycoides
• Models/M_pneumoniae – Mycoplasma pneumoniae
• Models/NatShorkie – Native yeast genome models

Each directory contains fine-tuned Keras (.h5) models, organized by cross-validation fold and ensemble member.

Usage

All models are compatible with the ExoShorkie codebase:

https://github.com/OrensteinLab/ExoShorkie

Please refer to the main repository for loading, inference, and evaluation instructions.