Blog Archives

List of Bioinformatics Workshops and Training Resources

April 4, 2013
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I frequently get asked to recommend workshops or online learning resources for bioinformatics, genomics, statistics, and programming. I compiled a list of both online learning resources and in-person workshops (preferentially highlighting those where workshop materials are freely available online):List of Bioinformatics Workshops and Training ResourcesI hope to keep the page above as up-to-date as possible....

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"Document Design and Purpose, Not Mechanics"

February 12, 2013
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If you ever write code for scientific computing (chances are you do if you're here), stop what you're doing and spend 8 minutes reading this open-access paper:Wilson et al. Best Practices for Scientific Computing. arXiv:1210.0530 (2012). (Direct link t...

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Twitter Roundup, January 4 2013

January 4, 2013
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I've said it before: Twitter makes me a lazy blogger. Lots of stuff came across my radar this week that didn't make it into a full blog post. Here's a quick recap:PLOS Computational Biology: Chapter 1: Biomedical Knowledge IntegrationAssuring the quali...

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Computing for Data Analysis, and Other Free Courses

January 2, 2013
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Coursera's free Computing for Data Analysis course starts today. It's a four week long course, requiring about 3-5 hours/week. A bit about the course:In this course you will learn how to program in R and how to use R for effective data analysis. Y...

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Getting Genetics Done 2012 In Review

December 31, 2012
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Here are links to all of this year's posts (excluding seminar/webinar announcements), with the most visited posts in bold italic. As always, you can follow me on Twitter for more frequent updates. Happy new year!New Year's Resolution: Learn How to Code...

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Differential Isoform Expression With RNA-Seq: Are We Really There Yet?

December 17, 2012
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Differential Isoform Expression With RNA-Seq: Are We Really There Yet?

In case you missed it, a new paper was published in Nature Biotechnology on a method for detecting isoform-level differential expression with RNA-seq Data:Trapnell, Cole, et al. "Differential analysis of gene regulation at transcript resolution with RN...

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Learn R and Python, and Have Fun Doing It

September 24, 2012
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If you need to catch up on all those years you spent not learning how to code (you need to know how to code), here are a few resources to help you quickly learn R and Python, and have a little fun doing it.First, the free online Coursera course Co...

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DESeq vs edgeR Comparison

September 18, 2012
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DESeq vs edgeR Comparison

Update (Dec 18, 2012): Please see this related post I wrote about differential isoform expression analysis with Cuffdiff 2.DESeq and edgeR are two methods and R packages for analyzing quantitative readouts (in the form of counts) from high-throughput e...

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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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