Check out this month's table of contents in Nature Methods. It contains a series of five commissioned Reviews discuss the challenges of visualizing biological data and the visualization tools available to biologists working with genomes, alignments and phylogenies, macromolecular structures, images and systems biology data.
Suppose you have billions of reads from a hot new sequencing machine and you want to simultaneously align these reads and call SNPs very quickly on the cheap. Check out an open source tool called Crossbow and the recent paper in Genome Biology.
In a previous tutorial I showed you how to create plots faceted by the level of a third variable using ggplot2. A commenter asked about using faceted plots and viewports and reminded me of this function I found in the ggplot2 Google group. The arrange function below is similar to using par(mfrow=c(r,c)) in base graphics to put more than one plot in the same image window.
I joined the Ritchie Lab back in 2007, and even though it's only been three years away from the bench, I've forgotten much of what I learned back in biochem classes. I'm giving a talk on lipid genetics next week, and I found the Wiley Essential Biochemistry website very helpful for brushing up on some basic lipoprotein biology. There are 27 chapters covering a broad range of topics from enzyme kinetics to phosphofructokinase regulation.
Time for a little shameless self-promotion. I'll be giving a talk in genetics interest group next week. "Using GWAS in an EMR-linked biobank to explore genetic and environmental determinants of HDL cholesterol" Thursday, March 11, 2010 Noon-1pm 206 PRBGetting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.
A while back I went to one of these specifically for writing an F31 NRSA fellowship application. Ended up getting one the first try. I thought the workshop was helpful. This looks a little more general, but may give you some ideas about getting external funding that isn't necessarily from NIH. Grant &
Thomas Lasko, MD, PhD, from Google Inc., Mountain View CA, will be giving a seminar next week entitled: "Spectral Anonymization Data" March 3, 2010 12:00 - 1:00 p.m. 214 Light Hall Abstract: The great challenge of data anonymization is to condition a dataset for public release such that it remains scientifically useful, but it does not disclose sensitive information about the individuals it describes.
The Pharmacology department's student invited seminar is coming up next week. Last time the students invited an excellent speaker from Washington to talk about AAAS fellowships. This year's student invited speaker is James S. Bernstein, Director, Government and Public Affairs for the American Society for Pharmacology and Experimental Therapeutics.
The first post on Getting Genetics Done was one year ago today. To celebrate, here are the top 10 most viewed posts since GGD launched last year. Incidentally, nine of the ten are tutorials on how to do something in R. Thanks to all the readers and all the commenters for sharing your thoughts!
Doug Robinson (JMP Academic Division, SAS Institute) is giving a presentation of the JMP Genomics software from SAS illustrating data analysis for genetics, expression, and copy number variation studies. Agenda includes: CNV analysis, merging CNV data sets of continuous traits, and QC, analysis, and downstream applications of expression studies.
If you read the previously mentioned "synthetic associations" paper in PLoS Bio by Dickson et al. in David Goldstein's group, be sure to read this brief commentary written by Pat Sullivan at UNC offering a different point of view.