Code from "Germline variants affect lung-to-tumor transcription dynamics, NSCLC outcomes"

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)
• Deconvolution analysis (see deconvolution folder)
• Comparison between common somatic alterations and germline effects on tumor gene expression (see somatic_vs_germline folder)
• Quantification of expression heterogeneity and relationship to Delta-eQTL analysis (see transcription_heterogeneity 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.