Blog Archives

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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Scatterplot matrices in R

July 25, 2011
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Scatterplot matrices in R

I just discovered a handy function in R to produce a scatterplot matrix of selected variables in a dataset. The base graphics function is pairs(). Producing these plots can be helpful in exploring your data, especially using the second method below.Try...

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Steal This Blog!

June 22, 2011
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Steal This Blog!

I wanted to contribute any content and code I post here to the R Programming Wikibook so I made a slight change to the Creative Commons license on this blog. All the written content is now cc-by-sa and all the code here is still open source BSD. So fee...

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More Command-Line Text Munging Utilities

May 19, 2011
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More Command-Line Text Munging Utilities

In a previous post I linked to gcol as a quick and intuitive alternative to awk. I just stumbled across yet another set of handy text file manipulation utilities from the creators of the BEAGLE software for GWAS data imputation and analysis. In additio...

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More Command-Line Text Munging Utilities

May 19, 2011
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More Command-Line Text Munging Utilities

In a previous post I linked to gcol as a quick and intuitive alternative to awk. I just stumbled across yet another set of handy text file manipulation utilities from the creators of the BEAGLE software for GWAS data imputation and analysis. In additio...

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Accessing Databases From R

May 9, 2011
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Accessing Databases From R

Jeffrey Breen put together a useful slideshow on accessing databases from R. I use RODBC every single day to access my own local MySQL server from R. I've had trouble with RMySQL, so I've always used RODBC instead after setting up my localhost MySQL se...

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Accessing Databases From R

May 9, 2011
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Jeffrey Breen put together a useful slideshow on accessing databases from R. I use RODBC every single day to access my own local MySQL server from R. I've had trouble with RMySQL, so I've always used RODBC instead after setting up my localhost MySQL se...

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PLINK/SEQ for Analyzing Large-Scale Genome Sequencing Data

May 4, 2011
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PLINK/SEQ for Analyzing Large-Scale Genome Sequencing Data

PLINK/SEQ is an open source C/C++ library for analyzing large-scale genome sequencing data. The library can be accessed via the pseq command line tool, or through an R interface. The project is developed independently of PLINK but it's syntax will be f...

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PLINK/SEQ for Analyzing Large-Scale Genome Sequencing Data

May 4, 2011
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PLINK/SEQ is an open source C/C++ library for analyzing large-scale genome sequencing data. The library can be accessed via the pseq command line tool, or through an R interface. The project is developed independently of PLINK but it's syntax will be f...

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Annotated Manhattan plots and QQ plots for GWAS using R, Revisited

April 25, 2011
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Annotated Manhattan plots and QQ plots for GWAS using R, Revisited

Last year I showed you how to create manhattan plots, and later how to highlight regions of interest, using ggplot2 in R. The code was slow, required a lot of memory, and was difficult to maintain and modify.I finally found time to rewrite the code usi...

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