jinmiaochenlab/batch-effect-removal-benchmarking repository overview

⁠Description

This docker contains data used in paper: A benchmark of batch-effect correction methods for single-cell RNA sequencing data⁠. The related scripts can be found here: https://github.com/JinmiaoChenLab/Batch-effect-removal-benchmarking⁠.

⁠Pre-Download

Please confirm that:

1. You have installed docker as the instructions: Install Docker Desktop on Mac⁠, Install Docker Desktop on Windows⁠ and Docker engine for Linux⁠ according to your OS.

2. You are in "docker" or "sudo" group if you are using Mac or Linux OS.

⁠Usage

To download the data, please follow these steps:

1. Go to target folder
2. run sudo docker create --name batcheffect jinmiaochenlab/batch-effect-removal-benchmarking to download docker image.
3. run sudo docker cp batcheffect:/batch_effect/ ./ to copy the data to current folder.
4. run sudo docker container rm batcheffect; docker image rm jinmiaochenlab/batch-effect-removal-benchmarking to delete docker image.
5. If you are in "docker" group, then you don't need to use sudo.

⁠If you encounter any issue to install or run docker, please consult your system administrator. It will save you a lot of time.