Monday, April 11, 2011

Monday Links: 23andMe, RStudio, PacBio+Galaxy, Data Science One-Liners, Post-Linkage RFA, SSH

Lately I haven't written as many full length posts as usual, but here's a quick roundup of a few links I've shared on Twitter (@genetics_blog) over the last week:

First, 23andMe is having a big DNA Day Sale ($108) for the kit + 1 year of their personal genome subscription service https://www.23andme.com/.

Previously mentioned R IDE RStudio released a new beta (version 0.93) that includes several new features and bugfixes. Among the new features, my favorites include the ability to customize the pane layout, and the included {manipulate} package that facilitates interactive plotting: http://bit.ly/gR9ir8.

The Pacific Biosciences open-source Analysis suite is out: http://j.mp/f9QP0F (genomeweb subscribers only), and you can watch a video tutorial (free) on Galaxy-PacBio integration here: http://j.mp/i1FzEm.

If you already have existing genotype/phenotype data on families you've collected, you might check out this new RFA from NHLBI and NHGRI: “Life After Linkage: the Future of Family Studies” http://1.usa.gov/dR9gHb: This FOA issued by NHLBI and NHGRI solicits applications which integrate novel molecular data with existing genotype and phenotype data in families to identify and characterize  genes influencing complex disorders.  Applications for this program should have previously examined families with some genotyping and phenotypes available.  Proposals may utilize focused ascertainment from families, for example, using risk profile, extreme phenotypes or families contributing heavily to genomic signals.  The program may support the addition of targeted or whole genome sequencing, exon sequencing, copy number variants (CNVs), expression profiling, metabolomics, epigenomics,  and/or novel biomarkers.  This may require additional sample collection and/or reconsent.  Applications should include a strong analytic component focused on bioinformatics and integration of multiple data types.

Data Science Hand Tools http://oreil.ly/hyhb6Z. This piece includes nice demonstrations of using grep, awk, cut, colrm, sort, uniq, wc, find, xargs, and other simple and flexible UNIX one-liners to do some serious data munging.

A new paper from Lucia Hindorff, Elizabeth Gillanders, and Teri Manolio at NHGRI: Genetic architecture of cancer & complex diseases: Lessons learned & future directions http://1.usa.gov/h28J2A

Bioinformatics special issue includes acompilation of all Bioinformatics papers on Next-Generation Sequencing http://bit.ly/DcfAm

And finally, simple instructions for setting up password-free SSH login http://linuxproblem.org/art_9.html

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Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License.