In order to make your analysis pipeline transparent and reproducible, in this class you’ll use R Markdown and Knitr to wrap up all your code and outputs (figures, tables, etc) together in a dyanmic document that can be placed in your lab notebook or published as a supplementary file in your manuscript.


  • understand how to construct a basic R markdown document
  • transform our course code into an Rmarkdown report
  • make an interactive Rmarkdown flexdashboard to display your data


The essentials - brings togther ‘the essential’ code chunks from our previous scripts.





Blog post on Knitr by Karl Broman

Other examples of markdown in action

Supplementary code file from a recent Nature Immunology paper

Supplementary code file from my lab’s recent transcriptome paper.

Make your own CV in markdown - uses the Vitae and Scholar packages in R.

This course website - Each page on the course website is just a simple markdown document.