Getting Genetics Done

A few weeks ago the 2014 AMIA Translational Bioinformatics Meeting (TBI) was held in beautiful San Francisco.  This meeting is full of grea...

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 ...

Manhattan plots have become the standard way to visualize results for genetic association studies, allowing the viewer to instantly see sig...

Since the near beginning of genome-wide association studies, the PLINK software package (developed by Shaun Purcell’s group at the B...

Here are links to all of this year's posts (excluding seminar/webinar announcements), with the most visited posts in bold italic . As al...

Thanks to the excellent work of Lucia Hindorff and colleagues at NHGRI, the GWAS catalog provides a great reference for the cumulative re...

In general, the standard practice for correcting for population stratification in genetic studies is to use principal components analysis...

I’m a bit exhausted from a week of excellent science at ICHG. First, let me say that Montreal is a truly remarkable city with fantastic f...

Peter Visscher and colleagues have recently published a flurry of papers employing a new software package called GCTA to estimate the herita...

DNA genotyping and sequencing are getting cheaper every day . As Oxford Nanopore CTO Clive Brown recently discussed at Genomes Unzipped, wh...

I just read a helpful paper on pathway analysis and interactome reconstruction: Tieri, P., Fuente, A. D., Termanini, A., & Franceschi,...

In a previous post I linked to gcol as a quick and intuitive alternative to awk. I just stumbled across yet another set of handy text file ...

PLINK/SEQ is an open source C/C++ library for analyzing large-scale genome sequencing data. The library can be accessed via the pseq comman...

**** UPDATE, May 15 2014 ***** The functions described here have now been wrapped into an R package . View the updated blog post or see th...

I'm working on a project using next-gen sequencing to fine-map a genetic association in a gene region. Now that I've sequenced the r...

Hansong Wang, our biostats professor here at the Hawaii Cancer Center, generously gave me some R code that goes through a SNP annotation fil...

The *ABEL suite of R packages and software for genetic analysis has grown substantially since the appearance of GenABEL and the previously ...