This repo contains custom R codes used for figures in the manuscript "Transcriptional immunogenomic analysis reveals distinct immunological clusters in pediatric nervous system tumours".
This repo is linked to the CodeOcean capsule link: https://doi.org/10.24433/CO.0339991.v1
CBTN raw RNA and WGS data, variant and fusion calls are available upon request at kidsfirstdrc.org. TCGA and TARGET data can be accessed upon request through GDC (https://gdc.cancer.gov/).
Gene expression matrices, clinical metadata, T- and B- clonotype files, HLA types, predicted neopeptides, variant and fusion datasets and deconvolution outputs are available upon free registration at https://cavatica.sbgenomics.com/u/pughlab/immpedcan.
All processed data can be found in /data/ or as supplemental tables for the manuscript.
Arash Nabbi: arash.nabbi@uhnresearch.ca
Trevor J. Pugh: trevor.pugh@utoronto.ca