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Getting Genetics Done

Getting Things Done in Genetics & Bioinformatics Research
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AnnouncementsJournal ClubRecommended ReadingBiyolojik Bilimlerİngilizce
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Yazar Stephen Turner

Our Program in Computation Genomics Journal Club is starting again, now the 3rd Friday of each month. The next meeting is this Friday, April 16, at 3pm in the CHGR conference room. As usual, please bring in any articles you've found recently and give a brief overview of why you thought it was interesting.

GWASRSoftwareStatisticsBiyolojik Bilimlerİngilizce
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Yazar Stephen Turner

I recently did an analysis for the eMERGE network where I had lots of individuals from a small town in central Wisconsin where many of the subjects were related to one another. The subjects could not be treated as independent, but I could not use a family-based design either. I ended up using a mixed model approach using previously mentioned GenABEL.

GWASRSoftwareStatisticsBiyolojik Bilimlerİngilizce
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Yazar Stephen Turner

I've been using GenABEL for some time now for GWAS analysis using related individuals. It has an excellent set of functions for estimating a kinship matrix from a dense marker panel and then using this in a linear mixed effects model to allow for related individuals in the analysis of a quantitative trait.

AnnouncementsBiyolojik Bilimlerİngilizce
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Yazar Stephen Turner

A short announcement - my friend, colleague, running partner, and GGD contributor Will Bush is now an assistant professor in the Department of Biomedical Informatics, and investigator in the Center for Human Genetics Research here at Vanderbilt.Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.

RStatisticsTutorialsBiyolojik Bilimlerİngilizce
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Yazar Stephen Turner

The previously mentioned Regression Modeling Strategies short course taught by Frank Harrell is nearly over. Here are the handouts (PDF) from the course. Keep an eye out here, I'll be writing a few more posts in the near future on topics Frank covered in this course.Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.

NewsNoteworthy BlogsPolicyBiyolojik Bilimlerİngilizce
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Yazar Stephen Turner

A District Court handed down a summary judgment invalidating most of Myriad's claims to both the BRCA1 DNA sequence and the method of testing for early-onset familial breast and ovarian cancer. See Genetic Future and Genomics Law Report for analysis.Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.

AnnouncementsBiyolojik Bilimlerİngilizce
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Yazar Stephen Turner

VICC's retreat this year is Tuesday, May 11, 2010. The theme of the retreat looks interesting: "Genomic Approaches for Personalized Medicine." You can register free here. VICC retreat: Genomic Approaches for Personalized MedicineGetting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.

Ggplot2RVisualizationBiyolojik Bilimlerİngilizce
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Yazar Stephen Turner

Hadley Wickham, creator of ggplot2, has posted a 2 hour video on data visualization using R. You can find links to the videos and slides over at Revolutions Blog. Check back here soon. I am working with Hadley to arrange a day-long ggplot2 short course here at Vanderbilt this summer.

Ggplot2GWASRVisualizationBiyolojik Bilimlerİngilizce
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Yazar Stephen Turner

*** Update April 25, 2011: This code has gone through a major revision. Please see the updated code and tutorial here. *** A few months ago I showed you in this post how to use some code I wrote to produce manhattan plots in R using ggplot2. The qqman() function I described in the previous post actually calls another function, manhattan(), which has a few options you can set.