Publications by Stephen Turner
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 and p-value) into tabular format to publish beside a scatterplot matrix. The built-i...
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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 experiments such as RNA-seq or ChIP-seq. After alignment, reads are assigned to a feature, where ...
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Learn R and Python, and Have Fun Doing It
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 Computing for Data Analysis just started. The 4 week course is being taught by Roger Peng,...
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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 RNA-seq.” Nature Biotechnology (2012).THE PROBLEMRNA-seq enables transcript-level ...
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Getting Genetics Done 2012 In Review
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 CodeAnnotating limma Results with Gene Names for Affy MicroarraysYour Publications (...
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Computing for Data Analysis, and Other Free Courses
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. You will learn how to install and configure software necessary for a statistical prog...
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Twitter Roundup, January 4 2013
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 quality of next-generation sequencing in clinical laboratory practice : Nature Biot...
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"Document Design and Purpose, Not Mechanics"
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 to PDF).The paper makes a number of good points regarding software as a tool just...
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List of Bioinformatics Workshops and Training Resources
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 ...
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Automated Archival and Visual Analysis of Tweets Mentioning #bog13, Bioinformatics, #rstats, and Others
Automatically Archiving Twitter ResultsEver since Twitter gamed its own API and killed off great services like IFTTT triggers, I’ve been looking for a way to automatically archive tweets containing certain search terms of interest to me. Twitter’s built-in search is limited, and I wanted to archive interesting tweets for future reference and ...
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