Blog Archives

Course Materials from useR! 2013 R/Bioconductor for Analyzing High-Throughput Genomic Data

July 12, 2013
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At last week's 2013 useR! conference in Albacete, Spain, Martin Morgan and Marc Carlson led a course on using R/Bioconductor for analyzing next-gen sequencing data, covering alignment, RNA-seq, ChIP-seq, and sequence annotation using R. The course mate...

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Customize your .Rprofile and Keep Your Workspace Clean

July 2, 2013
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Like your .bashrc, .vimrc, or many other dotfiles you may have in your home directory, your .Rprofile is sourced every time you start an R session. On Mac and Linux, this file is usually located in ~/.Rprofile. On Windows it's buried somewhere in the R...

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Automated Archival and Visual Analysis of Tweets Mentioning #bog13, Bioinformatics, #rstats, and Others

May 15, 2013
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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 buil...

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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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