Posts Tagged ‘ Bioinformatics ’

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 »

Data Analysis for Genomics MOOC

February 20, 2014
By
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...

Read more »

There is no Such Thing as Biomedical "Big Data"

February 11, 2014
By
There is no Such Thing as Biomedical "Big Data"

At the moment, the world is obsessed with “Big Data” yet it sometimes seems that people who use this phrase don’t have a good grasp of its meaning.  Like most good buzz-words, “Big Data” sparks the idea of something grand and complicated...

Read more »

Coursera Specializations: Data Science, Systems Biology, Python Programming

January 22, 2014
By
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 ...

Read more »

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

December 31, 2013
By
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...

Read more »

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

December 18, 2013
By
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...

Read more »

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

December 9, 2013
By
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...

Read more »

Using Database Joins to Compare Results Sets

November 20, 2013
By
Using Database Joins to Compare Results Sets

One of the most powerful tools you can learn to use in genomics research is a relational database system, such as MySQL.  These systems are fairly easy to setup and use, and provide users the ability to organize and manipulate data and statistical...

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 »


Subscribe

Email:

  Subscribe