Capstone Title: Interaction of autophagy and oxidative stress products in cancer

Aim

Using the weighted-gene co-expression analysis to systematically investigate the potential interactions of autophagy and oxidative stress response gene products in the context of cancer with emphasis on quality reproducible analysis.

Objectives

• To familiarize the trainee with the essential tools for conducting an analysis
• To run a case study analysis for autophagy and oxidative stress interactions in cance
• To produce a reproducible report (article/presentation) summarizing the analysis

Timeline

• Week One
  • Reading and discussing an article similar to the target study
  • Introduction to the tools that will be used in the study
• Week Two
  • Reproducing an analysis from an article and identifying essential building blocks of writing a reproducible analysis
  • Defining a question, choosing the dataset, and planning the analysis
• Week Three
  • Refining the analysis and quality controlling the study
  • Producing the analysis finding in form of tables and graphs
• Week Four
  • Writing the analysis in a basic research article format
  • Preparing the final trainee presentation

Resources

• Literature
  • Target article: Ahmed et al., 2018
  • Packaging reproducible analysis: Marwick et al., 2018
• Tooling
  • Scripting: R, Introduction to R
  • Command line: Wikipedia, The unix workbench
  • Version control: Git, GitHub
  • Overleaf: Literate Programming, Introduction to Overleaf
• Presentation
  • Preparing a scientific presentation: Presentation template, How to give a scientific presentation
  • Writing a research article: Structuring a science paper, The art of editing