Although typically we focus on databases and algorithms in use in bioinformatics and genomics, there are some other tools that support this work that are crucial as well. The statistical software and computing tools associated with R fall into this category. Increasingly RStudio is being adopted by folks in genomics, and although we talked about R in the past, I hadn’t highlighted the RStudio interface before. But this really lowered the barrier to entry, and has changed the way to use R effectively, and it’s time to include this in our Video Tips of the Week.
In a previous tip we highlighted some training on R that was delivered in a webinar, by Heather Merk of Ohio State. So if you need an overall Introduction to R Statistical Software, that’s a good place to start. When you are ready to begin to work with R, though, you should consider trying out RStudio.
This overview video will demonstrate the basics of the interface for RStudio.
There’s more detail on many of the features of RStudio that they provide as well. And their Vimeo channel has a few more videos as well. Another thing about using RStudio is that there’s increasingly additional types of support coming from that front. A popular tip we did was on Slidify to make sides directly from RStudio.
RStudio is not just for genomics, though–it’s widely used in many fields that engage in statistical analysis. I was surprised to not find a lot of references to it in PubMed yet–some guidance and explainers in biotech, but I know it’s being widely used. You can see a lot of examples in use in Google Scholar. This includes several enthusiastic uses of RStudio in teaching situation: An Attractive Template of a Reproducible Data Analysis Document for an Awesome Class Project; and Teaching precursors to data science in introductory and second courses in statistics. I did find reference to a software review in an economics publication. And you can get a book to help if that’s how you like to learn more as well.
But if you haven’t had a chance to check out RStudio yet, I’d recommend it.
Gandrud, Christopher. Reproducible Research with R and R Studio. CRC Press, 2013.
Racine J.S. (2011). RStudio: A Platform-Independent IDE for R and Sweave, Journal of Applied Econometrics, 27 (1) 167-172. DOI: http://dx.doi.org/10.1002/jae.1278
Fertig, E. (2012) Getting Started in R.