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.

Bioconda

Installation via Bioconda is the preferred route of installation, and we highly recommend using conda. To install Scaden, use:

conda install -c bioconda scaden

It is always recommended to create a separate conda environment for installation.

pip

If you don't want to use conda, you can also install Scaden using pip:

pip install scaden

Docker

If you don't want to install Scaden at all, but rather use a Docker container, we provide that as well. You can pull the Scaden docker container with the following command (from Dockerhub):

docker pull kevinmenden/scaden

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.