Blog Archives

More on Exploring Correlations in R

August 28, 2012
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More on Exploring Correlations in R

About a year ago I wrote a post about producing scatterplot matrices in R. These are handy for quickly getting a sense of the correlations that exist in your data. Recently someone asked me to pull out some relevant statistics (correlation coefficient ...

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Plotting the Frequency of Twitter Hashtag Usage Over Time with R and ggplot2

July 17, 2012
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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 ...

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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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