Bioinformatics Bites: R tutorials for beginners

Today’s Bioinformatics Bite is based on a hypothetical question that I think a lot of people are afraid to ask:

I hear R is a great tool for doing bioinformatic analysis, but I have no idea how to code. How can I get started?

Well, I’d say the first step is to Install R.

This first installation installs the R coding language and a bare-bones editor to write and run code in.

If you want a nicer interface, I’d suggest installing R studio. which has a lot of bells and whistles that will made using R a lot easier. R Studio contains a text editor with highlighting, integrated help functions, an environment window that reminds you what variables you created and a console that allows you to execute your code right from the editor.

Rstudio

But how do you even know where to begin now that you have it installed? A good place to start for R basics is Swirl. Swirl is a tutorial system that you can use INSIDE R. All you have to do to install Swirl is type

install.packages(“swirl”)

inside the R console, and swirl will be automatically installed!

Now to run Swirl, just type

> library("swirl")
> swirl()

in the R console to load the swirl library and run the tutorials. Then you can pick from a variety of introductory tutorials that are closely linked to courses in the Johns Hopkins University Data Science Specialization on Coursera. Now we just need to get someone to write some Swirl tutorials for Bioconductor.

If you have any questions about how to set up R, don’t hesitate to Ask.

Tobin Magle,

Biomedical Sciences Research Support Specialist

tobin.magle@ucdenver.edu

2 thoughts on “Bioinformatics Bites: R tutorials for beginners

  1. Tobin, I developed an R-class which is online for the Department of Biostatistics and Informatics. It is available for credit to any student and also available for faculty , We use on of our PhD students to TA the course and work through the materials and example exercises. It is more oriented toward the statistics modules than Bioinformatics modules but might be very helpful to anyone starting with R. Have individuals contact Debashis Ghosh or Dr Gary Grunwald in the CSPH School of Public Health Biostatistics and Informatics.

    Dr D Lezotte

    Reply

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