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, Iorgulescu, Weiss, Merrell, Wu et al.(2024)

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.13942487)
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 ghannam_gbm_icb_manuscript directory.
5. Run the Jupyter and Rmarkdown notebooks in notebooks/.