Integrative analysis in head and neck cancer reveals distinct role of miRNome and methylome as tumour epigenetic drivers

Description

This repository contains code that generates results published in the "Integrative analysis in head and neck cancer reveals distinct role of miRNome and methylome as tumour epigenetic drivers" paper.

• src: Contains all the scripts and source code files.

Scripts

Here is a list of the directories included in this project:

• [core]: [Contains the main analysis that generates results for the main finding in the paper]

  • Exploratory_analysis_and_differential_expression.Rmd
  • Regulation_targets.Rmd
  • Integrative_analysis.Rmd

• [analysis]: [Contains additional analysis, not all neccessarily ended up published]

  • manuscript_plots.Rmd
  • survival_analysis.Rmd
  • tumor_supressors_from_TCGA.Rmd
  • ctat-vif-notes_pipeline_v2.txt
  • virus_finder.Rmd
  • HPV_effect.Rmd

• [TCGA_analysis]: [Contains code for analyzing TCGA data for HNSCC and comparison to our analysis]

  • exploratory_analysis.R
  • DM_limm_islands.R
  • TCGA_reanalysis.Rmd

• [utils.R] [Contains helper functions]

• [demultiplexing_RNAseq.sh]

Publication

If you would like to learn more about this project, please refer to our publication: [Integrative analysis in head and neck cancer reveals distinct role of miRNome and methylome as tumour epigenetic drivers ]. You can find the preprint of the publication here.

Related Data

Related data files are deposited on Fig share and ArrayExpress:

• RNA-seq, transcriptome
  • Fig share - link
  • ArrayExpress E-MTAB-13725 - link
• miRNA-seq, miRNome - link
• methylome link