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 ... [Read more...]

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...]

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...]

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 ... [Read more...]

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...]

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... [Read more...]

I use heatmaps quite a lot for visualizing data, microarrays of course but also DNA motif enrichment, base composition and other things. I particular like the heatmap.2 function of the gplots package. It has a couple of defaults that are a little ugly ... [Read more...]

I can never remember this R command, so I am going to post it here which probably means I will always remember it and never have to look it up here again.I sometimes want to find the location of a minimum or maximum value in a vector, so I ... [Read more...]

I love using TeXShop for GUI editing of LaTeX and particularly Sweave documents, but it is a pain not being able to get it to automatically generate the pdf output. Luckily I found this post which explains how to add a Sweave engine.Basically, make a f... [Read more...]

A colleague wanted to extract the median value from a survival analysis object, which turned out to be a pain as the value is not stored in the object, but calculated on the fly by a print method. __ library(survival)__ fit __ survfit(fit)Call: survfit(formula = fit)records n.max ... [Read more...]

Some things I write in perl some in R, sometime I use perl to write R and run R. One thing that I find very useful is the functionality of RSPerl which enables you to call R functions from within perl and on perl variables. It can also call perl ... [Read more...]

I was sent this R style guide, and think it looks like it might be a good idea. R can be pretty difficult to read, especially someone else's. [Read more...]

I use R and Bioconductor for most of my work. I am also increasingly replacing things I would have done before in Perl with R. One such example of this is the Bioconductor module biomaRt.As the name suggest it allows for access to BioMart via R. BioMart is a ... [Read more...]