gbm_icb_manuscript

Code for generating figures in the glioblastoma ICB manuscript of Ghannam et al.:

"Tumor Transcriptional Subtype is a Major Axis of Immune Checkpoint Blockade Response in Glioblastoma". Ghannam et al.(2025)

Regenerating the figures:

1. Clone this Git repository
2. Install python dependencies (listed in environment.yaml)
3. Download data from Zenodo (DOI: 10.5281/zenodo.17460015)
4. Unzip the data in this directory: tar -xvzf gbm_icb_data.tar.gz. At this point there should be a directory called data in the gbm_icb_manuscript directory.
5. Run each of the Jupyter (*.ipynb) and Rmarkdown (*.Rmd/*.qmd) notebooks in the notebooks/ directory. Each notebook generates one or more of the figures. (In contrast, the src directory contains helper functions employed by the Jupyter notebooks. These files do not need to be executed directly.)