Getting Genetics Done

I just returned from the  Genome Informatics meeting  at Cold Spring Harbor. This was, hands down, the best scientific conference I've ...

Three years ago I wrote a blog post on how to create manhattan plots in R . After hundreds of comments pointing out bugs and other issues, I...

Boston-based startup Curoverse has announced $1.5 million in funding to develop and support the open-source Arvados platform  for ...

Torsten Seemann compiled a list of minimum standards for bioinformatics command line tools , things like printing help when no commands are...

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 collaborate with several investigators on gene expression projects using both microarray and RNA-seq. After I show a collaborator which ge...

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

A couple of weeks ago I, with the help of others here at UVA , organized a Software Carpentry bootcamp , instructed by Steve Crouch , Ca...

Metagenomics is the study of DNA collected from environmental samples (e.g., seawater, soil, acid mine drainage, the human gut, sputum, pus...

It's happened to all of us. You read about a new tool, database, webservice, software, or some interesting and useful data, but when you...

I've said it before: Twitter makes me a lazy blogger. Lots of stuff came across my radar this week that didn't make it into a full ...

Coursera's free Computing for Data Analysis course starts today. It's a four week long course, requiring about 3-5 hours/week. A bi...

There's a new kid on the block for RNA-seq alignment. Dobin, Alexander, et al. "STAR: ultrafast universal RNA-seq aligner." ...

I'm a huge supporter of the Free and Open Source Software movement. I've written more about R than anything else on this blog, all ...

Lately I've been using the limma package often for analyzing microarray data. When I read in Affy CEL files using ReadAffy(), the resul...

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

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 ...

A while back Will showed you how to ditch Excel for awk , a handy Unix command line tool for extracting certain rows and columns from a text...

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...