Immune Biomarkers

Goal of Repository

• Share code used to produce results for "Five factors underlie response to immunotherapy" paper.

Organization

• 0_analyses contains all analyses.
• 1_figures produces paper figures (0_analyses run first).
• env contains the conda environments .yaml files used to analyses and figures.
• launch_pad contains scripts run all the analyses.
• mission_control specifies directory locations and contains helper files.
• ref contains VHIO processed data and gene sets used in analysis

Requirements to run

Pre-processed Hartwig Medical Foundation Data

• Main analyses relie on output from: https://github.com/bbglab/hartwig_biomarkers
• Requires data access approval: https://www.hartwigmedicalfoundation.nl/en/data/data-access-request/
• Hartwig data used for analyses was from data requst shared on August 9, 2022.

Downloaded non-Hartwig External Data

• For validation we used publically shared data from other studies.
• Need to download these external data and specify directory locations.
• Links to download external data are in 0_analyses/2_validation.

QMap and conda environments

• Jobs are submitted with the QMap tool from the bbglab: https://github.com/bbglab/qmap
• QMap tool calls conda environments stored in env folder.

Run it

• From this root directory:

$ python run.py