OV_Histotypes

Classification of Ovarian Cancer Histotypes

Generate RSF

The Report of Statistical Findings (RSF) can be generated by following the steps below:

1. Clone the repository to your local machine and open the project by navigating to the OV_Histotypes.Rproj R project file. RStudio will then be launched.
2. Run renv::restore() to restore all packages used in this project into a private library on your local machine. Note that there are two local packages otta and ottaOvca stored on the UBC TeamShare network drive I (\\files.ubc.ca\team\gpec\i) located at I:/cellar. Ensure you are connected to UBC MyVPN (myvpn.ubc.ca) first if running off site, otherwise renv::restore() should work if you are connected to the eduroam WiFi network.
3. Restart the RStudio session and the Build tab should now have a Render Book button. Click that button to generate HTML and PDF formats of the RSF, or use the dropdown menu to generate a specific format only.
4. The updated report files are generated in _book/. From the Terminal, run quarto publish gh-pages to publish the RSF to GitHub Pages, hosted on the gh-pages branch
5. RSF is generated at URL https://talhouklab.github.io/OV_Histotypes/

Classifier Pipeline

The classifier pipeline can be run by following the steps below:

1. Clone the repo to a GSC server. We recommend using the gphost10 server as it uses the newest Rocky 9 OS, configured to use R-4.5.2.
2. Follow Step 2 of [Generate RSF] to install R package dependencies. You'll need to use sftp/scp/rsync to transfer the local packages otta and ottaOvca to the server, and place them at ~/Cellar of your root directory. This path is specified in the environment variable RENV_PATHS_CELLAR in .Renviron.
3. SSH to the numbers server to submit SLURM jobs. This is the job management system that allows us to fire away a large number of scripts to worker nodes.
4. Open a new tmux session to run the pipeline in so that the SSH session doesn't timeout if it is running for a long time.
5. Navigate to pipeline/README.md to see all the different pipelines that can be run and how to obtain results
6. The outputs will be in output directory specified in pipeline/assets/params.sh. Parameters in this script can be modified as necessary to change the pipeline.