Reproducible data analysis and mind-blowing dynamic lab notebook entries using knitr and markdown in R

“Your best collaborator is you, six months ago. But you won’t answer to emails.”

How often do you find yourself looking through old analysis code from weeks or months ago? The ‘clear’ annotations you commented in the script are absolutely vague and non-instructive. You can’t find the code you used to plot a figure for a manuscript that you need to revise for submission.

Markdown is a literate computer language that allows for note-taking and straightforward text-to-everything conversion. The knitr package in R enables conversion of text documents, annotated code and in-line analysis to end-user documents, including .HTML and .PDF (LaTeX). Together, these techniques offer a novel platform that enables the generation of dynamic and reproducible research reports with full transparency.

Learn the technique within 5 minutes. Direct video link


  • Knitr package (..)
  • Bioinformaticians need lab notebooks too (..)
  • Electronic lab notebook (..)
  • Getting started with Rmardown, knitr and Rstudio (..)
  • Reflecting on five years of the open lab notebook (..)

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Improving reproducibility: approaching the individual researcher