We are on the road this week at a workshop in Southern California, so I am going to hand off my tip responsibilities to Lynn Jorde. Another session in the Current Topics in Genome Analysis 2012 course that has been organized by the NHGRI featured Lynn Jorde. Lynn delivered a lecture (about 1.5 hours long [...]
Today’s tip is on a new database based on data from a single interesting paper, SNPxGE2. With a large scale association study from HapMap data (269 individuals, 4 populations, over 500k SNPs and 15k expression profiles), the research reported: the computationally predicted human SNP-coexpression associations, that is, the differential co-expression between 2 genes is associated with the [...]
SNPexp is a nice simple tool that uses PLINK to calculate the correlation (p-value) between SNPs in a given range of locations in the genome, or alternatively a list of specific SNP rsIDs, and the expression of a gene of interest. It combines the data from these two datasets: the HapMap project and GENEVAR*. It provides [...]
Ok, I’m back from Thanksgiving and catching up on some emails and found a couple of news items I wanted to pass along. WikiGenes invitation to edit a Nature Genetics paper Here’s an interesting “experiment” I got notified about. You could potentially get authorship on this paper if you contribute to the development of this [...]
Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment… Shout out to Daniel MacArthur and Paul D. who sought us out at ASHG to say [...]
Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment… METAREP: JCVI Metagenomics Reports – an open source tool for high-performance comparative metagenomics. Hat tip to [...]
This next post in our continuing semi-regular Guest Post series is from Andrew Johnson, one of the developers and the concept designer of SNAP, SNP Annotation and Proxy Search which is hosted at the Broad Institute. If you are a provider of a free, publicly available genomics tool, database or resource and would like to convey [...]
HapMap has had a few minor updates to their browser, and importantly, new phase 3 data was released early last year (drafts of that data were released in 2008). Haploview, the downloaded software that allows the user to perform in depth LD and haplotype analysis, has been recently updated from version 4.1 to version 4.2. [...]
Interesting post from SNPedia blog (we mentioned being able to view SNPedia SNPS HapMap last year in a post) of the top 10 SNPs of the year. Of course, as they mention, it’s very subjective. Because they have chosen SNPs with serious health interest, I’ll semi-frivolously (because hey, no knowledge is necessarily “frivolous” nominate either: [...]
This is from the HapMap team for the human data (not the green HapMap I referenced recently). Older data is going to be removed from the HapMap.org browser and from BioMart. It will still be available in the ftp archive–but I just thought a heads-up was in order for folks who might not be on [...]
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