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Getting Genetics Done

Getting Things Done in Genetics & Bioinformatics Research
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AnnouncementsBiologieAnglais
Publié
Auteur Stephen Turner

GGD has a new look. I was inspired by Gina Trapani (Smarterware, Lifehacker) to remove any extra lines, links, and other "ink" that doesn't serve any purpose, and I hope the site appears cleaner and easier to read. I also wanted the extra horizontal space for larger images and avoid the dreaded side-scrolling in posts with lots of code like this one.

BioinformaticsLinuxRBiologieAnglais
Publié
Auteur Stephen Turner

*Edit March 12* Be sure to look at the comments, especially the commentary on Hacker News - you can supercharge the find|xargs idea by using find|parallel instead. --- Do you ever discover a trick to do something better, faster, or easier, and wish you could reclaim all the wasted time and effort before your discovery?

BioinformaticsPathwaysRVisualizationBiologieAnglais
Publié
Auteur Stephen Turner

I get a lot of requests in the core about running a "pathway analysis." Someone ran a handful of gene expression arrays, or better yet, ran an RNA-seq experiment (with replicates!). These, and many other kinds of high-throughput assays (GWAS, ChIP-seq, etc.) result in a list of genes and some associated p-value, fold change, or other statistic. Here's some R code to download public data from a study on susceptibility to colorectal cancer.

BioinformaticsRBiologieAnglais
Publié
Auteur Stephen Turner

I direct the Bioinformatics Core at the University of Virginia, and I'm hiring. Visit this link on the UVA Jobs website for more information. Here's the description: I'm Hiring - Bioinformatics Analyst in the UVA Bioinformatics CoreGetting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.

PubMedBiologieAnglais
Publié
Auteur Stephen Turner

I'm updating my CV and biosketch for a few grant applications, and for some time now, NIH has required you to include the PubMed Central ID for each article you publish that arose from NIH support. I only have a dozen or so papers indexed in PubMed, but I still wanted a way to do this automatically. If you have scores of publications, looking up all the PMCIDs could easily become a hassle. First, create an account at My NCBI.

BiologieAnglais
Publié
Auteur Stephen Turner

The winter Joint Techs meeting is next week in Baton Rouge. I'm not going, but I plan on participating via a netcast to see what's going on. Jim Bottum, Clemson's CIO, is moderating an entire day devoted to the topic Enhancing Infrastructure Support for Data Intensive Science. Of particular interest to me are the talks from 9:30-11am Tuesday January 24 from researchers and those supporting climatology, genomics, and the XSEDE projects.

BioinformaticsRSoftwareBiologieAnglais
Publié
Auteur Stephen Turner

Lately I've been using the limma package often for analyzing microarray data. When I read in Affy CEL files using ReadAffy(), the resulting ExpressionSet won't contain any featureData annotation. Consequentially, when I run topTable to get a list of differentially expressed genes, there's no annotation information other than the Affymetrix probeset IDs or transcript cluster IDs.

ProductivityRTutorialsBiologieAnglais
Publié
Auteur Stephen Turner

Farhad Manjoo at Slate has a good article on why you need to learn how to program. Chances are, if you're reading this post here you're already fairly adept at some form of programming. But if you're not, you should give it some serious thought.

RBiologieAnglais
Publié
Auteur Stephen Turner

I use this all the time, and the setup is dead simple. Follow the code below to load the RMySQL package, connect to a database (here the UCSC genome browser's public MySQL instance), set up a function to make querying easier, and query the database to return results as a data frame. Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.