Tutorial:Exploring OpenSNP - an RMarkdown report on crowdsourced genotypes and phenotypes
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8.0 years ago

"Exploring OpenSNP" is a project I did for an intro stats class. Although the bioinformatics component is a bit soft, It might be useful for beginners learning R, dplyr, ggplot, RMarkdown, and knitr. (and now it is Binder-enabled)

Report: http://leipzig.github.io/opensnp/

Source code: https://github.com/leipzig/opensnp

Genome wide association studies are designed to look for genetic markers, typically single nucleotide polymorphisms, in microarray or sequencing data associated with phenotypes – diseases or other physical characteristics. OpenSNP (https://opensnp.org) is a community “crowdsourced” project in which ordinary people can submit genotypes obtained from commercial direct-to-consumer genetic testing providers such as 23andme, along with whatever phenotypic descriptors – both physical (eye color, height) and behavioral (disposition, preferences) – that they choose to reveal.

Can we validate published genome-wide association studies of common human phenotypes using the relatively small volunteered data publicly available in OpenSNP?

SNP R • 2.4k views
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Nice work Jeremy!

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And just in time for the R course I have to give next week :) This is a great example of what can be done with some common R packages and a great idea!

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