Articles by nsaunders

Twitter coverage of the ISMB 2012 meeting: some statistics

August 15, 2012 | 0 Comments

OK, let’s do this: some statistics and visualization of the tweets for ISMB 2012. First, thanks to Stephen Turner who got things started in this post at his excellent blog, Getting Genetics Done. Subscribe to his feed if you don’t already do so. I’ve created a Github repository ... [Read more...]

My day out at #osddmalaria

May 10, 2012 | 0 Comments

Finally, I get around to telling you that… …on Friday 24th February, I took a day out from my regular job to attend a meeting on Open Source Drug Discovery for Malaria. I should state straight away that whilst drug discovery and chem(o)informatics are topics that I find ...
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R gotcha for the week

March 15, 2012 | 0 Comments

I use the biomaRt package from Bioconductor in almost every R session. So I thought I’d load the library and set up a mart instance in my ~/.Rprofile: On starting R, I was somewhat perplexed to see this error message: Twitter to the rescue. @hadleywickham told me to load ... [Read more...]

Simple plots reveal interesting artifacts

March 14, 2012 | 0 Comments

I’ve recently been working with methylation data; specifically, from the Illumina Infinium HumanMethylation450 bead chip. It’s a rather complex array which uses two types of probes to determine the methylation state of DNA at ~ 485 000 sites in the genome. The Bioconductor project has risen to the challenge with a (...
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A Friday round-up

December 1, 2011 | 0 Comments

Just a brief selection of items that caught my eye this week. Note that this is a Friday as opposed to Friday, lest you mistake this for a new, regular feature. 1. R/statistics ggbio A new Bioconductor package which builds on the excellent ggplot graphics library, for the visualization of ... [Read more...]

Interacting with bioinformatics webservers using R

September 8, 2011 | 0 Comments

In an ideal world, all bioinformatics tools would be made available via the Web as a web service with an API, as well as a standalone package to download for local use. This is rarely the case and sometimes, even where one or the other is available, factors such as ... [Read more...]

Popular topics at the BioStar Q&A site

August 23, 2011 | 0 Comments

Which topics are the most popular at the BioStar bioinformatics Q&A site? One source of data is the tags used for questions. Tags are somewhat arbitrary of course, but fortunately BioStar has quite an active community, so “bad” tags are usually edited to improve them. Hint: if your question ... [Read more...]

ISMB coverage on Twitter? It’s possible there was…

July 31, 2011 | 0 Comments

Peter writes: I wonder if part of the drop off is live bloggers moving to platforms like Twitter? I can tell you it seemed like there were almost as many tweets for one SIG (#bosc2011) as for the whole of #ISMB / #ECCB2011, and I personally didn’t post anything to ... [Read more...]

I can’t resist a word cloud: now using R!

July 28, 2011 | 0 Comments

The wordcloud package is word clouds for R with a difference: they look great. Of course, having just analysed online coverage of the ISMB conference, I had to run all 6 906 comments from the 2008-2011 meetings through some code. If you followed along via the Sweave code, I went as far ... [Read more...]

Analysis of ISMB coverage at FriendFeed: 2008 – 2011

July 27, 2011 | 0 Comments

ISMB/ECCB 2011 was held between July 15-19 this year and as in previous years, FriendFeed was used to cover the meeting. Last year, I wrote a post about how to use R to analyse the coverage. I was planning something similar for 2011 when I thought: we have 4 years of ISMB ... [Read more...]

R: calculations involving months

July 7, 2011 | 0 Comments

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...]

Syntax highlighting of R code at

May 20, 2011 | 0 Comments

If your WordPress blog is hosted at (like this one), you may know that source code in posts is formatted and highlighted using a shortcode, as explained here. Until recently, R was not on the list of supported languages (neither was Perl), but I noticed today that both ... [Read more...]

Friday fun with: Google Trends

May 19, 2011 | 0 Comments

Some years ago, Google discovered that when people are concerned about influenza, they search for flu-related information and that to some extent, search traffic is an indicator of flu activity. Google Flu Trends was born. Illness is sweeping through our department this week and I have succumbed. It’s not ... [Read more...]

Friday fun projects

May 14, 2011 | 0 Comments

What’s a “Friday fun project”? It’s a small computing project, perfect for a Friday afternoon, which serves the dual purpose of (1) keeping your programming/data analysis skills sharp and (2) providing a mental break from the grind of your day job. Ideally, the skills learned on the project are ... [Read more...]

R 2.12 to 2.13 package upgrade

April 14, 2011 | 0 Comments

If you: use Linux have just upgraded your R installation from 2.12 to 2.13 installed some/all of your packages in your home area (e.g. ~/R/i486-pc-linux-gnu-library/2.12) and… …are wondering why R can’t see them any more just do this: # at a shell prompt cp ~/R/i486-pc-linux-gnu-library/2.12 ~/R/... [Read more...]

Fixing aberrant files using R and the shell: a case study

April 7, 2011 | 0 Comments

Once in a while, you embark on what looks like a simple computational procedure only to encounter frustration very early on. “I can’t even read my file into R!” you cry. Step back, take a deep breath and take note of what the software is trying to tell you. ... [Read more...]

The RStudio IDE: first impressions are positive

February 28, 2011 | 0 Comments

Integrated development environments (IDEs) are software development tools, providing an interface that enables you to write, debug, run and view the output of your code. Whether you need an IDE or find them useful depends very much on your own preferences and style of working. In my own case for ...
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Analysis of retractions in PubMed

November 30, 2010 | 0 Comments

As so often happens these days, a brief post at FriendFeed got me thinking about data analysis. Entitled “So how many retractions are there every year, anyway?”, the post links to this article at Retraction Watch. It discusses ways to estimate the number of retractions and in particular, a recent ...
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Findings increasingly novel, scientists say…

October 29, 2010 | 0 Comments

…was the tongue-in-cheek title of an image that I posted to Twitpic this week. It shows the usage of the word “novel” in PubMed article titles over time. As someone correctly pointed out at FriendFeed, it needs to be corrected for total publications per year. It was inspired by a ...
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BioStar users (of the world, unite)

October 9, 2010 | 0 Comments

Egon writes: Can someone please plot the BioStar users on a Google Map? Sounds like a challenge. Let’s go. 1. Harvesting user IP addresses BioStar user profiles (here’s mine) include a location field. It’s free text and optional, which means that location is missing or inaccurate for many ...
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