NETMAP (single-cell gene regulatory networks using XAI)

Installation

The repository is installable using pixi and pip. If you want to try out netmap, you can clone the repository, and install a kernel via pixi. Note: We do not include torch and cupy. These need to be installed separately when using pip, and will be installed automatically when using pixi installation

Pixi installation

1. Download and setup pixi.sh.
2. Install the jupyer kernel which includes torch and cupy and netmap. You can then set pixi_netmap as a kernel in your jupyterlab, or vscode environment
3. You can add extra packages using pixi add my-package and reinstall the kernel to add extra packages.

git clone https://github.com/bionetslab/netmap
cd netmap
pixi run install-kernel

pip install

A local, editable install in a conda environment can be done as follows. You need to install extra denpendencies yourself e.g. torch, cupy depending on you system.

git clone https://github.com/bionetslab/netmap
cd netmap
conda create -n netmap_env
conda activate netmap_env
pip install -e .