Scgen

Introduction

scGen is a generative model to predict single-cell perturbation response across cell types, studies and species.

For more information, please check:

Home page: https://github.com/theislab/scgen

Versions

2.1.0

Commands

python
python3

Module

You can load the modules by:

module load biocontainers
module load scgen

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run scgen on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=scgen
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers scgen