Setup of the FlatST environment

FlatST is a method for achieving high-efficiency clustering of spatial transcriptomes built on the pytorch framework. It can run normally on both Windows and linux systems. We recommend that you create a new virtual environment and have pytorch installed.

Build the pytorch framework and PyG

[1]:

# bash
# conda create -n FlatST python==3.10
# conda activate FlatST
# pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu121

Download FlatST from github repository

[2]:

# bash
# cd your/FlatST/path
# git clone https://github.com/CHENszu/FlatST.git
# cd FlatST
# ls -a

Configure FlatST

[3]:

# bash
# python setup.py build
# python setup.py install