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Immunogenomic analysis of pediatric nervous system tumours

This repo contains custom R codes used for figures in the manuscript "Transcriptional immunogenomic analysis reveals distinct immunological clusters in pediatric nervous system tumours".

How to run

This repo is linked to the CodeOcean capsule link: https://doi.org/10.24433/CO.0339991.v1

Data availability

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.

Contact

Arash Nabbi: arash.nabbi@uhnresearch.ca

Trevor J. Pugh: trevor.pugh@utoronto.ca