Tag Archives: R statistics

Video Tip of the Week: RStudio as an interface for using R

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.

RStudio Overview – 1:30 from RStudio, Inc. on Vimeo.

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.

Quick links:

RStudio: http://www.rstudio.com/

R: http://www.r-project.org/

RSeek: an R-specific search engine http://www.rseek.org (hat tip Elana Fertig’s handy intro slide deck)

References:

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.

Video Tips of the Week: Annual Review IV, 2nd half

As you may know, we’ve been doing these video tips-of-the-week for FOUR years now. We have completed around 200 little tidbit introductions to various resources from last year, 2011 (yep, it’s 2012 now). At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

You can see past years’ tips here: 2008 I2008 II2009 I2009 II2010 I2010 II. The summary of the first half of 2011 is available from last week.

July 2011

July 6: Prioritizing genes using the Gene Prioritization Portal

July 13: PolySearch, searching many databases at once

July 20: Human Epigenomics Visualization Hub

July 27: The new SIB Bioinformatics Resource Portal

 

August 2011

August 3: SNPexp, correlation between SNPs and gene expression 

August 10: CompaGB for comparing genome browser software

August 17: CoGe, comparing genomes revisited

August 24: Domain Draw for quick motif diagrams

August 31: From UniProt to the PSI SBKB and back again

 

September 2011

September 7: Plant comparative genomics using Plaza

September 14: phiGENOME for bacteriophage genome exploration

September 21: Getting flanking sequences of genomic locations

September 28: Introduction to R statistical software 

 

October 2011

October 5: VnD resource for genetic variation and drug information

October 12: Track Hubs in UCSC Genome Browser

October 19: Mitochondrial Transcriptome GBrowser 

October 26: Variation data from Ensembl

 

November 2011

November 2: MizBee Synteny Browser

November 9: The new database of genomic variants: DGV2

November 16: MapMi, automated mapping of microRNA loci

November 23: BioMart’s new central portal

November 30: Phosphida, a post-translational modification database

December 2011

December 7: VarSifter, for identifying key sequence variations

December 14: Big changes to NCBI’s genome resources

December 21: eggNOG for the Holidays (or to explore orthologous genes)

December 28: Video Tips of the Week: Annual Review IV (first half of 2011)