In order to document the code and results from a bioinformatics workflow you’ll be introduced to R Markdown and Knitr, and will use these tools 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.
- learn the basics of Rmarkdown and dynamic documents
- learn how to construct a basic R markdown document
- use the ‘essential’ code chunks from the course to populate an Rmarkdown report
- make a flexdashboard the incorporates graphics and code
Rmarkdown_template.Rmd - a skeletal template that you can fill out with the code ‘essentials’ that we covered in class.
Rmarkdown_essentials.Rmd - same template as above, but already filled in with essentials
flexdashboard_essentials.Rmd - a different style of Rmarkdown that puts the focus on creating a dashboard of graphics. Particularly powerful when combined with the interactive graphs we produced during the course.
Other examples of markdown in action
This course website - Each page on the course website is just a simple markdown document.