research diary

R: calculations involving months

July 7, 2011 | nsaunders

Ask anyone how much time has elapsed since September last year and they’ll probably start counting on their fingers: “October, November…” and tell you “just over 9 months.” So, when faced as I was today with a data frame (named dates) like this: How to add a 7th column, with ... [Read more...]

Beware of rogue header files (Bioconductor installation)

May 11, 2010 | nsaunders

Just a short note concerning a “gotcha”. As I have many times before, I opened an R console on my newly-upgraded (to lucid 10.04) Ubuntu machine, typed source(“”) and began a Bioconductor install with biocLite(). Only this time, I saw this: Error in dyn.load(file, ... [Read more...]

Experiments with igraph

April 21, 2010 | nsaunders

Networks – social and biological – are all the rage, just now. Indeed, a recent entry at Duncan’s QOTD described the “hairball” network representation as the dominant cultural icon in molecular biology. I’ve not had occasion to explore networks “professionally”, but have always been fascinated by both networks and the ...
[Read more...]

BioMart (and biomaRt)

March 26, 2010 | nsaunders

I’ve been vaguely aware of BioMart for a few years. Inexplicably, I’ve only recently started to use it. It’s one of the most useful applications I’ve ever used. The concept is simple. You have a set of identifiers that describe a biological object, such as a ... [Read more...]

A new twist on the identifier mapping problem

January 11, 2010 | nsaunders

Yesterday, Deepak wrote about BridgeDB, a software package to deal with the “identifier mapping problem”. Put simply, biologists can name a biological entity in any way that they like, leading to multiple names for the same object. Easily solved, you might think, by choosing one identifier and sticking to it, ... [Read more...]

A brief survey of R web interfaces

November 29, 2009 | nsaunders

I’m looking at ways to provide access to R via a web application. First rule: see what’s available first, before you reinvent the wheel. It’s not pretty. From the R Web Interfaces FAQ: Software Brief notes Rweb Page last updated 1999. Of the 3 example links on the page ... [Read more...]

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