Please also have a look at our multi-omics multi-task DL freamwork 👀: OmiEmbed
The FIRST GANs-based omics-to-omics translation framework
Xiaoyu Zhang ([email protected])
Data Science Institute, Imperial College London
OmiTrans is a generative adversarial networks (GANs) based omics-to-omics translation framework.
Paper Link: https://arxiv.org/abs/2111.13785
- CPU or NVIDIA GPU + CUDA CuDNN
- Python 3.6+
- Python Package Manager
- Python Packages
- PyTorch 1.2+
- TensorBoard 1.10+
- Tables 3.6+
- prefetch-generator 1.0+
- Git 2.7+
- Clone the repo
git clone https://github.com/zhangxiaoyu11/OmiTrans.git
cd OmiTrans
- Install the dependencies
- For conda users
conda env create -f environment.yml conda activate omitrans
- For pip users
pip install -r requirements.txt
- Put the gene expression data (A.tsv) and DNA methylation data (B.tsv) in the default data path (./data)
- Train and test using the default settings
python train_test.py
- Check the output files
cd checkpoints/test/
- Visualise the metrics and losses
tensorboard --logdir=tb_log --bind_all
If you use this code in your research, please cite our paper.
@misc{zhang2021omitrans,
title={OmiTrans: generative adversarial networks based omics-to-omics translation framework},
author={Xiaoyu Zhang and Yike Guo},
year={2021},
eprint={2111.13785},
archivePrefix={arXiv},
primaryClass={q-bio.GN}
}
Please also have a look at our multi-omics multi-task DL freamwork 👀: OmiEmbed
This source code is licensed under the MIT license.