Installation

Scaden be easily installed on a Linux system, and should also work on Mac. There are currently two options for installing Scaden, either using Bioconda or via pip.

pip

To install Scaden via pip, simply run the following command:

pip install scaden

Bioconda

Bioconda installation is currently not supported for the newest Scaden versions, but this will hopefully change soon. It is therefore highly recommended to install via pip.

conda install -c bioconda scaden

Docker

If you don't want to install Scaden at all, but rather use a Docker container, we provide that as well. For every release, we provide two version - one for CPU and one for GPU usage. To pull the CPU container, use this command:

docker pull ghcr.io/kevinmenden/scaden/scaden

For the GPU container:

docker pull ghcr.io/kevinmenden/scaden/scaden-gpu

Webtool (beta)

We now also provide a webtool for you:

https://scaden.ims.bio

It comes with pre-generated training datasets for several tissues. You only need to upload the epxression data for prediction. Please not that this is still in beta.