Update Friday, May 14, 2010: See this newer post on LocusZoom. If you caught Cristen Willer's seminar here a few weeks ago you saw several beautiful figures in the style of a manhattan plot, but zoomed in around a region of interest, with several other useful information overlays.
Here are the papers we talked about in yesterday's Journal Club: PLoS Biol. 2010 Jan 26;8(1):e1000294. Rare variants create synthetic genome-wide associations. See my previous coverage of this paper and the comments. Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB. PLoS Genet. 2010 Jan;6(1):e1000798.
Frank Harrell is teaching his 3-session short course on regression modeling strategies using R here at Vanderbilt next month. Frank is a professor and chair of the Vanderbilt Biostatistics Department, and the author of several massively popular R libraries, including Design, rms, and the indispensable Hmisc.
We're restarting the PCG Journal Club again Monday February 8 at 4pm in the CHGR conference room. Most of you who usually attend are familiar with the format, but if not, bring any papers you've read recently and give a brief (i.e. 2 minute) overview of the paper and why you thought it was interesting. No slides allowed.
If you were here for any of the talks Rick Myers has given here at Vanderbilt over the last few years you'll remember all the interesting biomedical research going on at his company, HudsonAlpha. Their spring symposium is March 30, 8am-6pm, at the HudsonAlpha institute in Huntsville, AL. It's FREE, and poster sessions are open to all students and postdocs.
Vanderbilt 2nd year grad students: Here is the study guide I made for studying for my general knowledge phase I qualifying exam. I'd recommend making your own, but this may help you with a place to start. You can download it at the link below. Update January 25, 2013 : I've uploaded the link to Figshare for a more permanent home.
If you caught Soumya Raychaudhuri's seminar last week you heard a lot about the tool he developed at the broad called GRAIL - Gene Relationships Across Implicated Loci. You've got GWAS results and now you want to prioritize SNPs to follow up in replication or functional studies.
"The hunt for the genetic roots of common diseases has hit a blank wall." ...quoting the first sentence in Nicholas Wade's New York Times article reviewing this PLoS Biology research paper by David Goldstein and his colleagues at Duke University. Also be sure to see Richard Robinson's synopsis of this paper, both published this week in PLoS Bio.
Soumya Raychaudhuri is the lead author on the GRAIL paper in Nature Genetics. GRAIL (Gene Relationships Across Implicated Loci) is software available from the Broad Institute and looks like an interesting way to prioritize SNPs for followup. I'll cover it here in the future, but in the meantime, check out this seminar this Wednesday.
Found this nice way to visually summarize contingency tables using ggplot2 in R on Hadley Wickham's ggplot2 cheat sheet. Using the same data in my previous post on making scatterplots in small multiples, I'll demonstrate how to use ggfluctuation() to make a fluctuation plot.
**** UPDATE, May 15 2014 ***** The functions described here have now been wrapped into an R package. View the updated blog post or see the online package vignette for how to install and use. If you'd still like to use the old code described here, you can access this at version 0.0.0 on GitHub.