Narendran Laboratory, Arnie Charbonneau Cancer Institute, Alberta Children's Hospital and University of Calgary, Calgary, Alberta, Canada

Repository associated with the project:

The Impact of Primary Immunodeficiency Informed Molecular Landscape on the Biology and Prognosis of Refractory Childhood and Adult Malignancies. Son Tran, Aru Narendran. Canadian Society of Allergy and Clinical Immunology (CSACI) 2020 Summer Studentship Project.

Corresponding author email: son.tran@ucalgary.ca

This repository contains R code for the curation of RNAseq data from tumour and normal tissue samples obtained from TCGA and GTEx, respectively, and provided by the recount2 project through the TCGAbiolinks Bioconductor/R package. Differential expression analysis (DEA) is performed using the limma-voom method with cut-offs at fold change > 2 or < -2 and p-value < 10e-16. Gene ontology (GO) enrichment analysis was performed using the pathfindR Bioconductor/R package. Project codes matching corresponding tumour and normal tissues are provided in Project_Codes.xlsx. PID-related genes were curated from the Fulgent Genetics 'Comprehensive Primary Immunodeficiency NGS Panel' and is provided in Panel_PIDGenes.xlsx.