WGA Viewer software from Duke University

A genome-wide association (GWA) study often involves analyzing the effects of 100,000s of single nucleotide polymorphisms (SNPs) on a disease outcome or trait. Visualizing such high density data can often prove tricky, especially if the investigator is interested in specific regions.

I have recently discovered a free tool called WGAviewer from the Duke University (http://people.genome.duke.edu/~dg48/WGAViewer/) that can greatly help with the visualization part (it does not perform any analysis). The software is based on Java so should be platform independent (I only used and tested it for Windows so far). Some of the key features includes:

1. QQ plots
2. Manhattan plots with *interactive zoom* in and out
3. Zoom to a region by gene name or region easily and visualize results
4. Ablity to select and annotate the top N snps
5. Automatic update of annotation on Ensembl and HapMap data
6. Calculate LD linkage for a particular region etc
7. Take publication quality snapshot pictures

One of the hassles I found was formatting the data for input. The documentations suggest several ways of making the data input using MAP files etc in the manual. However, the easiest way I found was to simply create a space-separated ASCII file (using R or even Excel) with the following columns: rsid, chromosome (1-22, X, Y, XY, M), Map (coordinate on the chromosome) and -logP (log base 10 of p-values).

SNP chromosome Map -logP
MitoA10045G M 10045 2.04858284222835
MitoT9900C M 9900 0.233064674990652
MitoT9951C M 9951 0.0641728753170715
rs1000000 12 125456933 1.16139248878691
rs10000010 4 21227772 0.149317624784192
rs10000023 4 95952929 1.15832462919552
rs10000030 4 103593179 0.106028436059944
rs10000041 4 165841405 0.221366644208304
rs1000007 2 237416793 0.213983677592946
...

You will need to create and load one file per analysis which is bit annoying if you have many analyses to visualize. I hope they add new features to visualize and (even better) compare different results in the near future. Imagine being able to superimpose manhattan plots from two different studies or techniques together!

The Web is 20 years old and its impact on journal reference management

I got this email from a certain Anderson Brown on the BioConductor mailing list. It actually lists some useful tools after a slightly wordy introduction and before a sales pitch (actually WizFolio offers a free account limited to 100MB or 200 items). Enjoy!

Hi,

March 2009 marks the 20th anniversary of the invention of the Web.   Like all great inventions, it arises out of an unmet need that badly needed a solution.  Tim Berners-Lee foresaw the great potential that can be unlocked by connecting data across disparate operating systems.  You can see the full talk by Tim Berners-Lee as he explains it at: http://www.ted.com/talks/tim_berners_lee_on_the_next_web.html

Fast forward to 2004 when the term “Web 2.0” was first coined.  This term now generally has the connotation of instant “read-write” and increased connectivity on the Web as exemplified by applications like Facebook, MySpace and Twitter. How will such technology impact upon the busy scientists’ workflow in terms of searching, compiling, organizing, sharing and analyzing peer reviewed journal articles?  A new crop of journal reference management applications have emerged within the last 18 months.  The term “journal reference management” is used here as opposed to the older term “bibliographic management” to emphasize the importance of managing and linking the bibliographic data with the PDFs.

The biggest frustration for the busy scientists is the difficulty of locating and managing the PDFs from a set of bibliographic data.  I have listed a number of recently released journal reference management applications that addresses to a certain degree this frustration.

Zotero – A research tool that helps you gather, organize, and analyze sources. www.zotero.org

Labmeeting – Organize, search, and store your paper collection and lab protocols. www.labmeeting.com

Pubget – Similar to Pubmed, except you get the PDFs right away. www.pubget.com

Mendeley – Academic software for managing & sharing your research papers. www.mendeley.com

At WizFolio, we started 2 years ago with a vision of creating a web based application that would manage bibliographic data and PDFs with the same ease that you would MP3 files.  Tightly coupled with the application is a citation tool that the user can customize on-the-fly with instantaneous preview.  We invite you to give WizFolio Web 2.0 a try at www.wizfolio.com and appreciate any feedback and comments that will make the application better.