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The first GANs-based omics-to-omics translation framework

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OmiTrans

Please also have a look at our multi-omics multi-task DL freamwork 👀: OmiEmbed

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The FIRST GANs-based omics-to-omics translation framework

Xiaoyu Zhang ([email protected])

Data Science Institute, Imperial College London

Introduction

OmiTrans is a generative adversarial networks (GANs) based omics-to-omics translation framework.

Getting Started

Prerequisites

  • 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+

Installation

  • 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

Try it out

  • 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

OmiEmbed

Please also have a look at our multi-omics multi-task DL freamwork 👀: OmiEmbed

License

This source code is licensed under the MIT license.