Reproducible Research Using Rmarkdown – NGS2015 Week 3

Tutorial by Marian Schmidt, PhD candidate at the University of Michigan and Software Carpentry instructor.

Fun presentation! Have used knitR and Rmarkdown for analysis script files before, but I didn’t even know that github could be accessed through the RStudio interface. Appreciated spending time on these tasks discussing how to automate, generate report, and documenting workflow.

However, I couldn’t actually get my RStudio to connect to my github account. (See bottom explanation and screenshot with errors.) Any help or suggestions for how to proceed with this would be greatly appreciated! Google results didn’t come up with much, but probably missing something. Otherwise, could make and push .Rmd files to github via commandline, great.


Marian’s Link, great Key Resources listed on the page, go look!

How is everyone feeling? Who is Amy Cuddy? Do a power pose!


What do you need to reproduce Figure?
– data
– metadata
– programs and parameters
– error bars
– explanation of methods
– pipeline workflow
– explanations for legend (what does “a” and “ab” mean, e.g.)
– versions of software and packages used

Producing a figure removes the figure from the scientific code used to generate the figure. Unless you have someone looking at your code, using it to produce similar figures. Let’s keep figures and code connected.

Suggestion for hackathons with people using similar code to put in different datasets, test, everyone is thinking about the code, using the code, and making sure it is robust.

Write code for yourself in 6 months, so that you will like yourself. 🙂

Post your code online! (Yes, you really need to do this…)

Cannot automate tasks or make science reproducible with .xls spreadsheets with notes and color coding. We’ve all seen this from colleagues. It’s OK to suggest to people you see doing this that there is a better way. Discussion for how to do this with a positive angle. For example: “Your data are cool. There is an easy way that requires R or Python to automate what you are doing. I am happy to help if you are interested.” If someone closer to you personally, like a labmate, shame and humor can be used. 🙂

Use pre-existing libraries and packages when possible. Groups of people testing these functions, then goes out into ‘Rsphere’.

Where are your files? If you wanted to go to a project, and look at the most current results you are working on. Where are they? Could you send a link to collaborators?

Last fall, conference to discuss how to make science more reproducible. Suggested this file structure:

Computing notebooks should be as ubiquitous and thorough as wet lab notebooks. This is SO important. Document all of these things for every single project at all steps:

  • Document your methods and workflows
  • Document the origin of all data in your project directory
  • Document when and how you downloaded the data
  • Record data version info
  • Record software version info with session_info()

You can use an Rmarkdown file to do this. Using inline code to make creation of tables much easier if the data change. Write pdf() and images. Relative paths instead of absolute paths. Use seed.seed() for randomizations. Parts of my workflow to change:

      • session_info
      • absolute paths
      • saving figures with pdf() instead of by hand
      • write code as though I’m sharing it
      • comment moreIn github, make repository.



Here’s where the problem started:

From RStudio, must go to Preferences and specify Git executable. You should then be able to connect your github repository to your RStudio and push changes directly from the RStudio GUI. Unfortunately, I got derailed and my RStudio showed this error message,


ProductName:	Mac OS X
ProductVersion:	10.9.5
BuildVersion:	13F34

Even though my git is installed and functional on the commandline, path to git executable input to RStudio will not work and keeps indicating that git is not detected on the system path. I even deleted RStudio, downloaded the lastest version (since mine was old). It still could not detect git in system path. What to do?


Here is my git and path:



Had lots of help trying to figure this out during the tutorial and could proceed just not with GUI. Something weird is going on.

From the commandline, can push files to github repo so really not a big deal. Here is some of the output from the practice script we did as a class, yay .Rmd works!

(This .html file is viewable from the web from the NGS_Reproducibility repo by adding “gh-pages” branch in this repo,then accessing via server name.)

Suggestion for educator to look up and read publications on Peer Instruction: Dr. Eric Mazur, Physics Instructor at Harvard:


About Lisa Johnson

PhD candidate at UC Davis in Molecular, Cellular, and Integrative Physiology
This entry was posted in Genomics Workshop, github, R, reproducibility, workshops. Bookmark the permalink.

2 Responses to Reproducible Research Using Rmarkdown – NGS2015 Week 3

  1. Pingback: Past Year as a Junior Bioinformatician in Perspective | Lisa Johnson Cohen

  2. Pingback: Intro git – Lab meeting | Lisa Johnson Cohen

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