Tutorial_setup.txt

Tutorial: How to set up the environment for LETSmix

This tutorial will guide you through the steps to set up the environment for LETSmix.

Step 1: download and unzip files from GitHub:https://github.com/ZhanYangen/LETSmix
$ git clone https://github.com/ZhanYangen/LETSmix.git
$ cd LETSmix

Step 2: create a new conda environment and activate it
$ conda create --name LETSmix python=3.8
$ conda activate LETSmix

Step 3: install the required packages
3.1. torch gpu version (here is an example for CUDA 10.2)
$ pip3 install -i https://pypi.tuna.tsinghua.edu.cn/simple torch torchvision torchaudio --extra-index-url https://download.pytorch.org/whl/cu102

3.2 other required packages
$ pip3 install -i https://pypi.tuna.tsinghua.edu.cn/simple --user scanpy==1.9.1 scipy==1.10.1 Pillow==8.4.0 scikit-learn==1.0.1 \
                                                                  scikit-image==0.21.0 anndata==0.8.0 matplotlib==3.4.3 \
                                                                  pandas==1.4.0 numpy==1.22.0

Now you can start using LETSmix and run the example.ipynb