Blog Archives

Visualize coverage for targeted NGS (exome) experiments

March 20, 2014
By
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...

Read more »

Software Carpentry at UVA, Redux

March 12, 2014
By
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, ...

Read more »

Data Analysis for Genomics MOOC

February 20, 2014
By

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...

Read more »

Coursera Specializations: Data Science, Systems Biology, Python Programming

January 22, 2014
By

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...

Read more »

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

December 31, 2013
By

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...

Read more »

Archival and analysis of #GI2013 Tweets

November 4, 2013
By
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 ...

Read more »

Real-time streaming differential RNA-seq analysis with eXpress

October 31, 2013
By
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 ...

Read more »

Analysis of #ASHG2013 Tweets

October 28, 2013
By
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...

Read more »

Google Developers R Programming Video Lectures

August 5, 2013
By

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...

Read more »

Archival, Analysis, and Visualization of #ISMBECCB 2013 Tweets

July 24, 2013
By
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 ...

Read more »