eturkes/tau-vulnerability repository overview

⁠Tau Vulnerability

⁠This analysis is a work-in-progress

Multiomics analysis to explore selective vulnerability to tauopathy.

To obtain the raw data and pre-computed results, please download this Google Drive folder:
The folder should then be renamed gdrive and placed in the top-level of this project.

For reproducibility, we provide several options for replicating the environment used in the original analysis:

⁠1. Docker

This approach requires Docker installation and setup https://www.docker.com/⁠.
The simplest command is to run run_all.R non-interactively with the following:

docker-compose up all

If one wishes to use RStudio, first create a .env file with the port you would like to use, as so:

PORT=8787

Then open RStudio with:

docker-compose up rstudio

If the Docker container is being launched on a remote machine, an SSH tunnel like the one below will be needed:

ssh -N -L 8787:localhost:8787 user@ip-address

⁠2. Singularity

This approach is similar to using Docker except with a Singularity wrapper to meet the security requirements common in high-performance computing (HPC).
Similar to before, run_all.R is called non-interactively with:

sh ./singularity.sh all

To use RStudio, no .env file is needed, it is instead included in the command:

sh ./singularity.sh rstudio 8787

As before, an SSH tunnel is required if connecting remotely.