Installation

In this tutorial, we will demonstrate how to install scMagnifier and set up the required runtime environment for its execution.
Here we would like to clarify one point: if you only intend to run it on single-batch or multi-batch datasets, you only need to install the scMagnifier environment; if you want to run it on spatial transcriptomic datasets, you need to install both scMagnifier and stagate_scMagnifier environment.

Step 1: Set up the scMagnifier and stagte_scMagnifier environments

Create scMagnifier environment.

cd scMagnifier_package
conda env create -f /env/scMagnifier.yml 

Create stagate_scMagnifier environment (only required for spatial transcriptomic dataset analysis).

conda env create -f /env/stagate_scMagnifier.yml 

Step2: Install scMagnifier

Install scMagnifier in scMagnifier environment

conda activate scMagnifier
cd scMagnifier_package
pip install . --no-deps

Install scMagnifier in stagate_scMagnifier environment

conda activate stagate_scMagnifier
cd scMagnifier_package
pip install . --no-deps
cd STAGATE-main
python setup.py build
python setup.py install