Blog Archives

Scraping organism metadata for Treebase repositories from GOLD using Python and R

Scraping organism metadata for Treebase repositories from GOLD using Python and R I recently wanted to get hold of habitat/phenotype/sequencing metadata for the individual organisms of an archived Treebase project.) The GOLD database holds more than 18000 full genomes. For many of these it provides pretty good metadata (GOLDcards) which are indirectly linked to...

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Two R tutorials for beginners

Two R tutorials for beginners I am currently in the process of rescuing some of the pages from my now defunct datajujitsu.co.uk blogger blog and moving to this Github/Clojure/Bootstrap version. I also today gave a tutorial to the University of Manche...

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Functional programming in R

Functional programming in R

Functional programming in R This post is based on a talk I gave at the Manchester R User Group on functional programming in R on May 2nd 2013. The original slides can be found here This post is about functional programming, why it is at the heart of the R language and how it can hopefully help you...

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Develop in RStudio, run in RScript

Develop in RStudio, run in RScript I have been using RStudio Server for a few months now and am finding it a great tool for R development. The web interface is superb and behaves in almost exactly the same way as the desktop version. However, I do have one gripe which has forced me to change my working...

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Mapping academic collaborations in Evolutionary Biology

Mapping academic collaborations in Evolutionary Biology

Mapping academic collaborations in Evolutionary Biology This post is a repubication of a visualisation I did in 2011 for my (now defunct) datajujitsu.co.uk blog. It was a naive first attempt at web-scraping from an academic publishers website. It was done before I was aware of the problems surrounding access to, and text-mining of, online academic content hosted by...

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