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Code from "Germline variants affect lung to tumor transcription dynamics, NSCLC relapse and mortality"

This repository contains code for eQTL analysis and it's downstream analysis and for the survival GWAS analysis. R and Julia were used as main analysis softwares.

  • eQTL analysis and fine-mapping was performed (see qtltools folder)
  • Enrichment of eVariants in functional annotations was performed (see ChromHMM_enrich folder)
  • Enrichment of eGenes in cell type specific gene sets was performed (see HPA_gene_sets_enrich folder)
  • Transcription factor binding sites were assessed (see TFBS_disrupt folder)
  • Differetial expression analysis was performed (see DEG folder)
  • Module-QTL analysis was performed (see module_qtl folder)
  • Survival GWAS analysis was performed (see survival_gwas folder)

The utils folders contains the code for convert_to_hgnc and plink_bed_encoding_to_genotype functions.

Warning : path to data files are only an indication for script readability, eventual users of this code should replace the paths in the scripts by theirs.