Blog Archives

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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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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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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Coursera Specializations: Data Science, Systems Biology, Python Programming

January 22, 2014
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I first mentioned Coursera about a year ago, when I hired a new analyst in my core. This new hire came in as a very competent Python programmer with a molecular biology and microbial ecology background, but with very little experience in statistics. I got him to take Roger Peng's Computing for Data Analysis course...

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Jeff Leek’s non-comprehensive list of awesome things other people did in 2013

December 31, 2013
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Jeff Leek, biostats professor at Johns Hopkins and instructor of the Coursera Data Analysis course, recently posted on Simly Statistics this list of awesome things other people accomplished in 2013 in genomics, statistics, and data science.At risk of s...

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Archival and analysis of #GI2013 Tweets

November 4, 2013
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Archival and analysis of #GI2013 Tweets

I archived and analyzed all Tweets containing #GI2013 from the recent Cold Spring Harbor Genome Informatics meeting, using my previously described code.Friday was the most Tweeted day. Perhaps this was due to Lior Pachter's excellent keynote, "Stories ...

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