sc_virus

Regulatory motif analysis workflow in a single-cell setup

Set up environment

1. To set up the environment for this project, you'll need to have conda installed.
2. Create the conda environment running the following:

   conda env create -f environment.yaml

3. Activate the environment and check the installation

   conda activate sc_virus
   conda list
   

Running miReact

Specify according paths in code/02run_mireact.R and run code/02run_mireact.sh in a cluster.

You can see more on the tutorial on how to run miReact here: https://github.com/muhligs/miReact

Running the workflow

Main workflow for sc_virus can be found in the snakefile. Scripts can be found in code/flow

Running the workflow in the cluster:

snakemake -j 10 --slurm --default-resources slurm_account=your_account

specify threads -j and slurm_account and add -n flag for a dry-run.