Consider adding a lesson on Rmarkdown

[naupaka]

We could port over (e.g.) the existing lesson from SWC's r-novice-gapminder as a place to start. I think knitr/Rmarkdown is a great way to tie back the analyses done with scripts and on the command line into a document that can be handed off to a collaborator.

[naupaka]

For the Stanford DC-genomics workshop, we had an Rmd template for what one of these might look like, incorporating the parsing of the VCF files and some munging.

[nlhuong]

I agree it would be very helpful to include a lesson on rmarkdown, as most people analyzing genomics data would like to generate reports with text comments and visualization together with the code.

I think it would also be beneficial to include a section in http://www.datacarpentry.org/R-genomics/00-before-we-start.html explaining the differences in document types RStudio offers, e.g. what are the differences and similarities between R Script/R Notebook/ R Markdown (even R presentation).
Following this how to generate html / pdf reports and what are the arguments one can set to get a nice looking report, e.g. toc, biocstyle etc.

[naupaka]

@nlhuong thanks for the feedback. We definitely plan to include a knitr/rmarkdown module in the R Genomics lessons that are in the early stages of development. Stay tuned!