Articles by Stephen Turner

Annotating limma Results with Gene Names for Affy Microarrays

January 17, 2012 | Stephen Turner

Lately I've been using the limma package often for analyzing microarray data. When I read in Affy CEL files using ReadAffy(), the resulting ExpressionSet won't contain any featureData annotation. Consequentially, when I run topTable to get a list of di...

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New Year’s Resolution: Learn How to Code

January 5, 2012 | Stephen Turner

Farhad Manjoo at Slate has a good article on why you need to learn how to program. Chances are, if you're reading this post here you're already fairly adept at some form of programming. But if you're not, you should give it some serious thought.Gina Trapani, former editor of ... [Read more...]

Query a MySQL Database from R using RMySQL

December 15, 2011 | Stephen Turner

I use this all the time, and the setup is dead simple. Follow the code below to load the RMySQL package, connect to a database (here the UCSC genome browser's public MySQL instance), set up a function to make querying easier, and query the database to ... [Read more...]

RNA-Seq & ChiP-Seq Data Analysis Course at EBI

December 8, 2011 | Stephen Turner

I just got this announcement from EMBL-EBI about an RNA-seq/ChIP-seq analysis hands-on course. Find the full details, schedule, and speaker list here.Title: Advanced RNA-Seq and Chip-Seq Data Analysis Course Date: May 1-4 2012 Venue: EMBL-EBI, Hinxton,... [Read more...]

An example RNA-Seq Quality Control and Analysis Workflow

December 6, 2011 | Stephen Turner

I found the slides below on the education page from Bioinformatics & Research Computing at the Whitehead Institute. The first set (PDF) gives an overview of the methods and software available for quality assessment of microarray and RNA-seq experim... [Read more...]

GEO2R: Web App to Analyze Gene Expression in GEO Datasets Using R

November 17, 2011 | Stephen Turner

Gene Expression Omnibus is NCBI's repository for publicly available gene expression data with thousands of datasets having over 600,000 samples with array or sequencing data. You can download data from GEO using FTP, or download and load the data direc...

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I’m Starting a New Position at the University of Virginia

September 8, 2011 | Stephen Turner

I just accepted an offer for a faculty position at the University of Virginia in the Center for Public Health Genomics / Department of Public Health Sciences. Starting in October I will be developing and directing a new centralized bioinformatics core ...

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Sync Your Rprofile Across Multiple R Installations

August 15, 2011 | Stephen Turner

Your Rprofile is a script that R executes every time you launch an R session. You can use it to automatically load packages, set your working directory, set options, define useful functions, and set up database connections, and run any other code you w...

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Friday Links: R, OpenHelix Bioinformatics Tips, 23andMe, Perl, Python, Next-Gen Sequencing

August 5, 2011 | Stephen Turner

I haven't posted much here recently, but here is a roundup of a few of the links I've shared on Twitter (@genetics_blog) over the last two weeks.Here is a nice tutorial on accessing high-throughput public data (from NCBI) using R and Bioconductor.Cloud...

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Scatterplot matrices in R

July 25, 2011 | Stephen Turner

I just discovered a handy function in R to produce a scatterplot matrix of selected variables in a dataset. The base graphics function is pairs(). Producing these plots can be helpful in exploring your data, especially using the second method below.Try...

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Steal This Blog!

June 22, 2011 | Stephen Turner

I wanted to contribute any content and code I post here to the R Programming Wikibook so I made a slight change to the Creative Commons license on this blog. All the written content is now cc-by-sa and all the code here is still open source BSD. So fee...

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More Command-Line Text Munging Utilities

May 19, 2011 | Stephen Turner

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 manipulation utilities from the creators of the BEAGLE software for GWAS data imputation and analysis. In additio...

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Accessing Databases From R

May 9, 2011 | Stephen Turner

Jeffrey Breen put together a useful slideshow on accessing databases from R. I use RODBC every single day to access my own local MySQL server from R. I've had trouble with RMySQL, so I've always used RODBC instead after setting up my localhost MySQL se... [Read more...]

PLINK/SEQ for Analyzing Large-Scale Genome Sequencing Data

May 4, 2011 | Stephen Turner

PLINK/SEQ is an open source C/C++ library for analyzing large-scale genome sequencing data. The library can be accessed via the pseq command line tool, or through an R interface. The project is developed independently of PLINK but it's syntax will be f... [Read more...]

Annotated Manhattan plots and QQ plots for GWAS using R, Revisited

April 25, 2011 | Stephen Turner

Last year I showed you how to create manhattan plots, and later how to highlight regions of interest, using ggplot2 in R. The code was slow, required a lot of memory, and was difficult to maintain and modify. I finally found time to rewrite the code u... [Read more...]

Using LaTeX for Math Formulas on the Web

April 20, 2011 | Stephen Turner

I love the idea of using R+LaTeX+Sweave for reproducible research. This is even easier now that R has a jazzy new IDE that supports Sweave syntax highlighting and automatic PDF generation. I know I'm going to take some flak for saying this, but let's ... [Read more...]

Using R + Bioconductor to Get Flanking Sequence Given Genomic Coordinates

April 12, 2011 | Stephen Turner

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 region in a small sample, I'm picking SNPs to genotype in a larger sample. When designing the genotyping assay the lab wi... [Read more...]

Monday Links: 23andMe, RStudio, PacBio+Galaxy, Data Science One-Liners, Post-Linkage RFA, SSH

April 11, 2011 | Stephen Turner

Lately I haven't written as many full length posts as usual, but here's a quick roundup of a few links I've shared on Twitter (@genetics_blog) over the last week:First, 23andMe is having a big DNA Day Sale ($108) for the kit + 1 year of their personal ...

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Prune GWAS data in R

March 29, 2011 | Stephen Turner

Hansong Wang, our biostats professor here at the Hawaii Cancer Center, generously gave me some R code that goes through a SNP annotation file (i.e. a mapfile) and selects SNPs that are at least a certain specified distance apart. You might want to do t...

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RStudio Keyboard Shortcut Reference PDF

March 21, 2011 | Stephen Turner

I recently started using RStudio, the amazing new IDE for R. You can view all of RStudio's keyboard shortcuts by going to the help menu, but I made this printable reference for myself and thought I'd share it. I only included the Windows shortcuts, and... [Read more...]

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Articles by Stephen Turner

Annotating limma Results with Gene Names for Affy Microarrays

New Year’s Resolution: Learn How to Code

Query a MySQL Database from R using RMySQL

RNA-Seq & ChiP-Seq Data Analysis Course at EBI

An example RNA-Seq Quality Control and Analysis Workflow

GEO2R: Web App to Analyze Gene Expression in GEO Datasets Using R

I’m Starting a New Position at the University of Virginia

Sync Your Rprofile Across Multiple R Installations

Friday Links: R, OpenHelix Bioinformatics Tips, 23andMe, Perl, Python, Next-Gen Sequencing

Scatterplot matrices in R

Steal This Blog!

More Command-Line Text Munging Utilities

Accessing Databases From R

PLINK/SEQ for Analyzing Large-Scale Genome Sequencing Data

Annotated Manhattan plots and QQ plots for GWAS using R, Revisited

Using LaTeX for Math Formulas on the Web

Using R + Bioconductor to Get Flanking Sequence Given Genomic Coordinates

Monday Links: 23andMe, RStudio, PacBio+Galaxy, Data Science One-Liners, Post-Linkage RFA, SSH

Prune GWAS data in R

RStudio Keyboard Shortcut Reference PDF

Articles by Stephen Turner

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