Publications by Stephen Turner
Visualize coverage for targeted NGS (exome) experiments
I’m calling variants from exome sequencing data and I need to evaluate the efficiency of the capture and the coverage along the target regions.This sounds like a great use case for bedtools, your swiss-army knife for genomic arithmetic and interval manipulation. I’m lucky enough to be able to walk down the hall and bug Aaron Quin...
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qqman: an R package for creating Q-Q and manhattan plots from GWAS results
Three years ago I wrote a blog post on how to create manhattan plots in R. After hundreds of comments pointing out bugs and other issues, I’ve finally cleaned up this code and turned it into an R package.The qqman R package is on CRAN: http://cran.r-project.org/web/packages/qqman/The source code is on GitHub: https://github.com/st...
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Using Volcano Plots in R to Visualize Microarray and RNA-seq Results
I’ve been asked a few times how to make a so-called volcano plot from gene expression results. A volcano plot typically plots some measure of effect on the x-axis (typically the fold change) and the statistical significance on the y-axis (typically the -log10 of the p-value). Genes that are highly dysregulated are farther to the lef...
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Collaborative lesson development with GitHub
If you’re doing any kind of scientific computing and not using version control, you’re doing it wrong. The git version control system and GitHub, a web-based service for hosting and collaborating on git-controlled projects, have both become wildly popular over the last few years. Late last year GitHub announced that the 10-million...
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An Annotated Online Bioinformatics / Computational Biology Curriculum
Two years ago David Searls published an article in PLoS Comp Bio describing a series of online courses in bioinformatics. Yesterday, the same author published an updated version, “A New Online Computational Biology Curriculum,” (PLoS Comput Biol 10(6): e1003662. doi: 10.1371/journal.pcbi.1003662).This updated curriculum has a supp...
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Bedtools tutorial from 2013 CSHL course
A couple of months ago I posted about how to visualize exome coverage with bedtools and R. But if you’re looking to get a basic handle on genome arithmetic, take a look at Aaron Quinlan’s bedtools tutorials from the 2013 CSHL course. The tutorial uses data from the Maurano et al exploration of DnaseI hypersensitivity sites in hun...
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Introduction to R for Life Scientists: Course Materials
Last week I taught a three-hour introduction to R workshop for life scientists at UVA’s Health Sciences Library.I broke the workshop into three sections:In the first half hour or so I presented slides giving an overview of R and why R is so awesome. During this session I emphasized reproducible research and gave a demonstration of u...
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Do your "data janitor work" like a boss with dplyr
Data “janitor-work”The New York Times recently ran a piece on wrangling and cleaning data:“For Big-Data Scientists, ‘Janitor Work’ Is Key Hurdle to Insights”Whether you call it “janitor-work,” wrangling/munging, cleaning/cleansing/scrubbing, tidying, or something else, the article above is worth a read (even though it implicitly ...
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UVA / Charlottesville R Meetup
TL;DR? We started an R Users group, awesome community, huge turnout at first meeting, lots of potential.—I’ve sat through many hours of meetings where faculty lament the fact that their trainees (and the faculty themselves!) are woefully ill-prepared for our brave new world of computing- and data-intensive science. We’ve started...
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R package to convert statistical analysis objects to tidy data frames
I talked a little bit about tidy data my recent post about dplyr, but you should really go check out Hadley’s paper on the subject.R expects inputs to data analysis procedures to be in a tidy format, but the model output objects that you get back aren’t always tidy. The reshape2, tidyr, and dplyr are meant to take data frames, munge them arou...
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