Installation

Environment setting (optional)

For using scASprofiler, we recommend creating a separated `conda environment`_ for easier and cleaner management of dependent packages, particularly pytorch, which are under active development.

The following command line in terminal (Linux or MacOS) will create a conda environment with name scasp.(tested on Python 3.10.9):

install

git clone https://github.com/1027victor/scASprofiler.git
cd scASprofiler
conda env create -f environment.yaml
conda activate scasp
pip install torch==2.7.0 torchvision==0.22.0 torchaudio==2.7.0 --index-url https://download.pytorch.org/whl/cu118
pip install .

Test

In order to test the installation, you could type scASprofiler-perp, scASprofiler-impute, scASprofiler-quantify. If you have any issues, please report them to the issue on scASprofiler issues.