Blog Archives

Unsuck your writing

April 8, 2014
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Unsuck your writing

I recently found this little gem of a web app that analyzes the clarity of your writing. Hemingway highlights long, complex, and hard to read sentences. It also highlights complex words where a simple one would do, and highlights adverbs, suggesting yo...

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Visualize coverage for targeted NGS (exome) experiments

March 20, 2014
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Visualize coverage for targeted NGS (exome) experiments

I'm calling variants from exome sequencing data and I need to evaluate the efficiency of the capture and the coverage along the target regions.This sounds like a great use case for bedtools, your swiss-army knife for genomic arithmetic and interval man...

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Software Carpentry at UVA, Redux

March 12, 2014
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Software Carpentry at UVA, Redux

Software Carpentry is an international collaboration backed by Mozilla and the Sloan Foundation comprising a team of volunteers that teach computational competence and basic programming skills to scientists. In addition to a suite of online lessons, ...

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Data Analysis for Genomics MOOC

February 20, 2014
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Data Analysis for Genomics MOOC

Last month I told you about Coursera's specializations in data science, systems biology, and computing. Today I was reading Jeff Leek's blog post defending p-values and found a link to HarvardX's Data Analysis for Genomics course, taught by Rafael Iriz...

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GNU Screen

January 30, 2014
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GNU Screen

This is one of those things I picked up years ago while in graduate school that I just assumed everyone else already knew about. GNU screen is a great utility built-in to most Linux installations for remote session management. Typing 'screen' at t...

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Coursera Specializations: Data Science, Systems Biology, Python Programming

January 22, 2014
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Coursera Specializations: Data Science, Systems Biology, Python Programming

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 ...

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How To Install BioPerl Without Root Privileges

January 13, 2014
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How To Install BioPerl Without Root Privileges

I've seen this question asked and partially answered all around the web. As with anything related to Perl, I'm sure there is more than one way to do it. Here's how I do it with Perl 5.10.1 on CentOS 6.4.First, install local::lib with bootstra...

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

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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Curoverse raises $1.5M to develop & support an open-source bioinformatics data analysis platform

December 18, 2013
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Curoverse raises $1.5M to develop & support an open-source bioinformatics data analysis platform

Boston-based startup Curoverse has announced $1.5 million in funding to develop and support the open-source Arvados platform for cloud-based bioinformatics & genomics data analysis.The Arvados platform was developed in George Church's lab by s...

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Biostar Tutorial: Cheat sheet for one-based vs zero-based coordinate systems

December 9, 2013
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Biostar Tutorial: Cheat sheet for one-based vs zero-based coordinate systems

Obi Griffith over at Biostar put together this excellent cheat sheet for dealing with one-based and zero-based genomic coordinate systems. The cheat sheet visually explains the difference between zero and one-based coordinate systems, as well as how to...

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