Blog Archives

R package to convert statistical analysis objects to tidy data frames

September 16, 2014
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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...

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UVA / Charlottesville R Meetup

September 11, 2014
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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...

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Do your "data janitor work" like a boss with dplyr

August 20, 2014
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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 denigrates the important work that your housekeeping staff does). It’s...

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Introduction to R for Life Scientists: Course Materials

July 7, 2014
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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. Du...

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Bedtools tutorial from 2013 CSHL course

June 24, 2014
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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 ...

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An Annotated Online Bioinformatics / Computational Biology Curriculum

June 13, 2014
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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):...

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Collaborative lesson development with GitHub

June 2, 2014
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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 popu...

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Using Volcano Plots in R to Visualize Microarray and RNA-seq Results

May 28, 2014
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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...

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qqman: an R package for creating Q-Q and manhattan plots from GWAS results

May 15, 2014
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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/stephenturner/qqmanIf you'd like to cite the...

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Visualize coverage for targeted NGS (exome) experiments

March 20, 2014
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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 man...

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