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...
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 ...
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):...
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...
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...
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...
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...
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, ...
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...
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...
Jobs for R users