Publications by Stephen Turner
I’m Hiring!
I direct the Bioinformatics Core at the University of Virginia, and I’m hiring. Visit this link on the UVA Jobs website for more information. Here’s the description:The University of Virginia Bioinformatics Core is seeking a full-time position as a bioinformatics analyst. The analyst will work with other core staff on grant-funded...
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Pathway Analysis for High-Throughput Genomics Studies
I get a lot of requests in the core about running a “pathway analysis.” Someone ran a handful of gene expression arrays, or better yet, ran an RNA-seq experiment (with replicates!). These, and many other kinds of high-throughput assays (GWAS, ChIP-seq, etc.) result in a list of genes and some associated p-value, fold change, or ot...
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find | xargs … Like a Boss
*Edit March 12* Be sure to look at the comments, especially the commentary on Hacker News – you can supercharge the find|xargs idea by using find|parallel instead.—Do you ever discover a trick to do something better, faster, or easier, and wish you could reclaim all the wasted time and effort before your discovery? I’ve had this happen many...
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Video Tip: Convert Gene IDs with Biomart
I get asked frequently how to convert from one gene identifier to another. This can be tricky, especially when relying on gene symbols, as Will pointed out in a previous post a few years ago. There are several tools that can do this, including DAVID and the previously mentioned new Biomart ID Converter, but I still prefer using the En...
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RNA-Seq Methods & March Twitter Roundup
There were lots of interesting developments this month that didn’t work their way into a full blog post. Here is an incomplete list of what I’ve been tweeting about over the last few weeks. But first I want to draw your attention to the latest manuscript for a new bioconductor package for doing RNA-seq in R.DEXSeq vs Cuffdiff. See...
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NSF BIGDATA webinar
If you’re doing any kind of big data analysis – genomics, transcriptomics, proteomics, bioinformatics – then unless you’ve been on vacation the last few weeks you’ve no doubt heard about the NSF/NIH BIGDATA Initiative (here’s the NSF solicitation and here’s the New York Times article about the funding opportunity). The...
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Stepping Outside My Open-Source Comfort Zone: A First Look at Golden Helix SVS
I’m a huge supporter of the Free and Open Source Software movement. I’ve written more about R than anything else on this blog, all the code I post here is free and open-source, and a while back I invited you to steal this blog under a cc-by-sa license.Every now and then, however, something comes along that just might be worth payi...
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How to Stay Current in Bioinformatics/Genomics
A few folks have asked me how I get my news and stay on top of what’s going on in my field, so I thought I’d share my strategy. With so many sources of information begging for your attention, the difficulty is not necessarily finding what’s interesting, but filtering out what isn’t. What you don’t read is just as important...
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Fix Overplotting with Colored Contour Lines
I saw this plot in the supplement of a recent paper comparing microarray results to RNA-seq results. Nothing earth-shattering in the paper – you’ve probably seen a similar comparison many times before – but I liked how they solved the overplotting problem using heat-colored contour lines to indicate density. I asked how to repr...
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Plotting the Frequency of Twitter Hashtag Usage Over Time with R and ggplot2
The 20th annual ISMB meeting was held over the last week in Long Beach, CA. It was an incredible meeting with lots of interesting and relevant talks, and lots of folks were tweeting the conference, usually with at least a few people in each concurrent session. I wrote the code below that uses the twitteR package to pull all the tweets...
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