Epigenomics and RNAseq in R

To use this notebook

1. Go to ood.ccv.brown.edu (you will need an Oscar account).
2. Go to 'Clusters' in the blue menu bar at the top and click the drop-down that says '>_OSCAR Shell Access'
3. Go to your home folder (cd ~)
4. Git clone the repo (`git clone https://github.com/compbiocore/ccv_bootcamp_epigenomics_rnaseq.git`)
5. Go back to ood.ccv.brown.edu and look under Interactive Apps in the blue menu bar and click on RStudio on Singularity under Expert GUIs.

Fill in the fields as follows:

• Account: leave blank\
• Partition: leave blank\
• Number of hours: 2\
• Num Cores: 1\
• Memory: 40\
• Singularity Container Path:/oscar/data/shared/databases/workshops/bootcamp_2025/ccv_bootcamp_epigenomics_rnaseq/ccv_bootcamp_epigenomics_rnaseq.sif\
• Package install Path: leave blank\
• Path for R Executable: ~/scratch\
• R Module: leave blank\
• Additional Data Path: /oscar/data/shared/databases/workshops/bootcamp_2025/DiffBind_Vignette
• Reservation: bootcamp

Once your job starts, click the button to connect to session.
At the top of the screen you'll see a menu bar that starts with 'file', click on 'file' and 'open file' and open the notebooks/index.qmd file in the repo you cloned.\

title:
tags:
analysts:
git_repo_url:
resources_used:
summary:
project_id:
year:
documentation_url:
website_section: