Blog Archives

Coursera Specializations: Data Science, Systems Biology, Python Programming

January 22, 2014
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I first mentioned Coursera about a year ago, when I hired a new analyst in my core. This new hire came in as a very competent Python programmer with a molecular biology and microbial ecology background, but with very little experience in statistics. I got him to take Roger Peng's Computing for Data Analysis course...

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Jeff Leek’s non-comprehensive list of awesome things other people did in 2013

December 31, 2013
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Jeff Leek, biostats professor at Johns Hopkins and instructor of the Coursera Data Analysis course, recently posted on Simly Statistics this list of awesome things other people accomplished in 2013 in genomics, statistics, and data science.At risk of s...

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Archival and analysis of #GI2013 Tweets

November 4, 2013
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Archival and analysis of #GI2013 Tweets

I archived and analyzed all Tweets containing #GI2013 from the recent Cold Spring Harbor Genome Informatics meeting, using my previously described code.Friday was the most Tweeted day. Perhaps this was due to Lior Pachter's excellent keynote, "Stories ...

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Real-time streaming differential RNA-seq analysis with eXpress

October 31, 2013
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Real-time streaming differential RNA-seq analysis with eXpress

RNA-seq has been performed routinely for at least 5+ years, yet there is no consensus on the best methodology for analyzing this data. For example, Eduardo Eyras's group recently posted a pre-print on methods to study splicing from RNA-seq, where this ...

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Analysis of #ASHG2013 Tweets

October 28, 2013
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Analysis of #ASHG2013 Tweets

I archived and anlayzed all Tweets with the hashtag #ASHG2013 using my previously mentioned code.Number of Tweets by date shows Wednesday was the most Tweeted day:The top used hashtags other than #ASHG2013:The most prolific users:And what Twitter analy...

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Google Developers R Programming Video Lectures

August 5, 2013
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Google Developers recognized that most developers learn R in bits and pieces, which can leave significant knowledge gaps. To help fill these gaps, they created a series of introductory R programming videos. These videos provide a solid foundation for p...

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Archival, Analysis, and Visualization of #ISMBECCB 2013 Tweets

July 24, 2013
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Archival, Analysis, and Visualization of #ISMBECCB 2013 Tweets

As the 2013 ISMB/ECCB meeting is winding down, I archived and analyzed the 2000+ tweets from the meeting using a set of bash and R scripts I previously blogged about.The archive of all the tweets tagged #ISMBECCB from July 19-24, 2013 is and ...

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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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