Blog Archives

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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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):...

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Collaborative lesson development with GitHub

June 2, 2014
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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 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 qqman package (appreciated but not required), please cite this pre-print: Turner, S.D. qqman: an R package…

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Unsuck your writing

April 8, 2014
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Unsuck your writing

I recently found this little gem of a web app that analyzes the clarity of your writing. Hemingway highlights long, complex, and hard to read sentences. It also highlights complex words where a simple one would do, and highlights adverbs, suggesting yo...

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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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Software Carpentry at UVA, Redux

March 12, 2014
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Software Carpentry at UVA, Redux

Software Carpentry is an international collaboration backed by Mozilla and the Sloan Foundation comprising a team of volunteers that teach computational competence and basic programming skills to scientists. In addition to a suite of online lessons, ...

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Data Analysis for Genomics MOOC

February 20, 2014
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Data Analysis for Genomics MOOC

Last month I told you about Coursera's specializations in data science, systems biology, and computing. Today I was reading Jeff Leek's blog post defending p-values and found a link to HarvardX's Data Analysis for Genomics course, taught by Rafael Iriz...

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