Posts Tagged ‘ Bioinformatics ’

GEO2R: Web App to Analyze Gene Expression in GEO Datasets Using R

November 17, 2011
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GEO2R: Web App to Analyze Gene Expression in GEO Datasets Using R

Gene Expression Omnibus is NCBI's repository for publicly available gene expression data with thousands of datasets having over 600,000 samples with array or sequencing data. You can download data from GEO using FTP, or download and load the data direc...

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A New Dimension to Principal Components Analysis

October 27, 2011
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A New Dimension to Principal Components Analysis

In general, the standard practice for correcting for population stratification in genetic studies is to use principal components analysis (PCA) to categorize samples along different ethnic axes.  Price et al. published on this in 20...

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I’m Starting a New Position at the University of Virginia

September 8, 2011
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I’m Starting a New Position at the University of Virginia

I just accepted an offer for a faculty position at the University of Virginia in the Center for Public Health Genomics / Department of Public Health Sciences. Starting in October I will be developing and directing a new centralized bioinformatics core ...

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Interacting with bioinformatics webservers using R

September 8, 2011
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Interacting with bioinformatics webservers using R

In an ideal world, all bioinformatics tools would be made available via the Web as a web service with an API, as well as a standalone package to download for local use. This is rarely the case and sometimes, even where one or the other is available, factors such as cost come into play. So

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Popular topics at the BioStar Q&A site

August 23, 2011
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Popular topics at the BioStar Q&A site

Which topics are the most popular at the BioStar bioinformatics Q&A site? One source of data is the tags used for questions. Tags are somewhat arbitrary of course, but fortunately BioStar has quite an active community, so “bad” tags are usually edited to improve them. Hint: if your question is “How to find SNPs”, then

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QTL Analysis in R

August 13, 2011
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QTL Analysis in R

See also: Part 1: QTL Analysis and Quantitative Genetics  Part 2: Statistical Methods for QTL Analysis The 'qtl' package in R allows you to implement QTL analysis using the methods I've previously discussed. The code below is adapted from Broman...

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Friday Links: R, OpenHelix Bioinformatics Tips, 23andMe, Perl, Python, Next-Gen Sequencing

August 5, 2011
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Friday Links: R, OpenHelix Bioinformatics Tips, 23andMe, Perl, Python, Next-Gen Sequencing

I haven't posted much here recently, but here is a roundup of a few of the links I've shared on Twitter (@genetics_blog) over the last two weeks.Here is a nice tutorial on accessing high-throughput public data (from NCBI) using R and Bioconductor.Cloud...

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ISMB coverage on Twitter? It’s possible there was…

July 31, 2011
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ISMB coverage on Twitter? It’s possible there was…

Peter writes: I wonder if part of the drop off is live bloggers moving to platforms like Twitter? I can tell you it seemed like there were almost as many tweets for one SIG (#bosc2011) as for the whole of #ISMB / #ECCB2011, and I personally didn’t post anything to FriendFeed but posted lots on

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I can’t resist a word cloud: now using R!

July 28, 2011
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I can’t resist a word cloud: now using R!

The wordcloud package is word clouds for R with a difference: they look great. Of course, having just analysed online coverage of the ISMB conference, I had to run all 6 906 comments from the 2008-2011 meetings through some code. If you followed along via the Sweave code, I went as far as generating the

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Analysis of ISMB coverage at FriendFeed: 2008 – 2011

July 27, 2011
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Analysis of ISMB coverage at FriendFeed: 2008 – 2011

ISMB/ECCB 2011 was held between July 15-19 this year and as in previous years, FriendFeed was used to cover the meeting. Last year, I wrote a post about how to use R to analyse the coverage. I was planning something similar for 2011 when I thought: we have 4 years of ISMB at FriendFeed now

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