Blog Archives

Fix Overplotting with Colored Contour Lines

July 6, 2012
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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...

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How to Stay Current in Bioinformatics/Genomics

May 29, 2012
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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...

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Stepping Outside My Open-Source Comfort Zone: A First Look at Golden Helix SVS

May 16, 2012
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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....

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NSF BIGDATA webinar

May 1, 2012
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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...

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RNA-Seq Methods & March Twitter Roundup

April 6, 2012
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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 manuscri...

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Video Tip: Convert Gene IDs with Biomart

March 14, 2012
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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 an...

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find | xargs … Like a Boss

March 9, 2012
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*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 c...

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Pathway Analysis for High-Throughput Genomics Studies

March 6, 2012
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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,...

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I’m Hiring!

February 24, 2012
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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 bio...

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Hadley Wickham: ggplot2 Webinar (Today!)

February 8, 2012
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Title: A Backstage Tour of ggplot2 with Hadley WickhamDate: Wednesday, February 8, 2012Time: 11:00AM - 12:00PM PacificPresenter: Hadley Wickham, Professor of Statistics, Rice UniversityRegister here.I used ggplot2 extensively a few years ago, but rever...

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