yilanbai/oligoformer repository overview

⁠User-friendly Docker image

The Docker image simplifies the installation and setup process, making it easy for users to get started with OligoFormer without worrying about dependencies and environment configuration.

⁠Prerequisites

• Docker⁠ installed on your machine.

⁠Installation

1. Pull the Docker Image:

   docker pull yilanbai/oligoformer:v1.0
   

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2. Run the Docker Container:

   docker run -it --name oligoformer-container -dt --restart unless-stopped yilanbai/oligoformer:v1.0 && docker exec -it oligoformer-container bash
   

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3. Access the OligoFormer Tool:

   Once inside the container, you can start using OligoFormer with the following command:

   oligoformer -h # help
   oligoformer # infer
   oligoformer -i 1 -i1 example.fa -i2 example_siRNA.fa # infer only interested siRNA(faster)
   oligoformer -off # infer with off-target prediction
   oligoformer -tox # infer with toxicity prediction
   oligoformer -off -tox # infer with off-target and toxicity prediction
   oligoformer -m 2 # mismatch input 19nt siRNA
   oligoformer -i 0 -t # test inter-dataset
   oligoformer -i 0 -s -t # test intra-dataset
   # We recommand you to run the following two commands on the patform with GPUs.
   oligoformer -i 0 # train inter-dataset
   oligoformer -i 0 -s # train intra-dataset
   

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