Blog Archives

Things I would tell a budding bioinformatician to learn.

July 7, 2011
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I recently read Ewan Birney's blog post, which I found echoed a lot of my own thoughts about the use of statistical in computational biology. I thought I would compile my own similar list but for bioinformatics  / computational biology in general. I have not been and in the field as long as Ewan and I certainly still...

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R: Basic R Skills – Splitting and Plotting

December 10, 2010
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R: Basic R Skills – Splitting and Plotting

I am giving a short R course next year, so I am going to make a series of blog posts to help get my thoughts and example code in order. The aim is to introduce people with little or no experience of R to the language with self contained examp...

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R: Basic R Skills – Splitting and Plotting

December 10, 2010
By
R: Basic R Skills – Splitting and Plotting

I am giving a short R course next year, so I am going to make a series of blog posts to help get my thoughts and example code in order. The aim is to introduce people with little or no experience of R to the language with self contained examp...

Read more »

R: Using RColorBrewer to colour your figures in R

December 8, 2010
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R: Using RColorBrewer to colour your figures in R

RColorBrewer is an R packages that uses the work from http://colorbrewer2.org/ to help you choose sensible colour schemes for figures in R. For example if you are making a boxplot with eight boxes, what colours would you use, or if you are drawing...

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R: Using RColorBrewer to colour your figures in R

December 8, 2010
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R: Using RColorBrewer to colour your figures in R

RColorBrewer is an R packages that uses the work from http://colorbrewer2.org/ to help you choose sensible colour schemes for figures in R. For example if you are making a boxplot with eight boxes, what colours would you use, or if you are drawing...

Read more »

R: Command Line Calculator using Rscript

June 18, 2010
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I currently use an awesome little bash trick to get a command line calculator that was posted on lifehacker, and that I blogged about previously.calc(){ awk "BEGIN{ print $* }" ;}You just add this to your .bashrc file and then you can use it ...

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R: Command Line Calculator using Rscript

June 18, 2010
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I currently use an awesome little bash trick to get a command line calculator that was posted on lifehacker, and that I blogged about previously.calc(){ awk "BEGIN{ print $* }" ;}You just add this to your .bashrc file and then you can use it ...

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R tip: Maximum screen width

April 19, 2010
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R can be annoying in that even if you stretch your terminal or R GUI session to a whole screen width it will still only show 80 characters width. This can make wide tables really hard to read. options(width=150)Use the options command width to set...

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R tip: Maximum screen width

April 19, 2010
By

R can be annoying in that even if you stretch your terminal or R GUI session to a whole screen width it will still only show 80 characters width. This can make wide tables really hard to read. options(width=150)Use the options command width to set...

Read more »

R: parallel processing using multicore package

April 14, 2010
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I have been meaning to look at adding some parallel processing to R as I have some scripts that are painfully slow and embarrassingly parallel. There seem to be a lot of packages around for doing parallel computing, listed here.I decided to look at mul...

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