Articles by nsaunders

Basic R: rows that contain the maximum value of a variable

February 12, 2013 | nsaunders

File under “I keep forgetting how to do this basic, frequently-required task, so I’m writing it down here.” Let’s create a data frame which contains five variables, vars, named A – E, each of which appears twice, along with some measurements: Now, let’s say we want only the ... [Read more...]

Addendum to yesterday’s post on custom CSS and R Markdown

August 27, 2012 | nsaunders

Updates from RStudio support: (1) “Thanks for reporting and I was able to reproduce this as well. I’ve filed a bug and we’ll take a look.” (2) Taking a further look, this is actually a bug in the Markdown package and we’ve asked the maintainer (Jeffrey Horner) to look ... [Read more...]

Custom CSS for HTML generated using RStudio

August 26, 2012 | nsaunders

People have been telling me for a while that the latest version of RStudio, the IDE for R, is a great way to generate reports. I finally got around to trying it out and for once, the hype is justified. Start with this excellent tutorial from Jeremy Anglim. Briefly: the ... [Read more...]

Twitter coverage of the ISMB 2012 meeting: some statistics

August 15, 2012 | nsaunders

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 | nsaunders

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 ...

[Read more...]

R gotcha for the week

March 15, 2012 | nsaunders

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 | nsaunders

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 (...

[Read more...]

A Friday round-up

December 1, 2011 | nsaunders

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 | nsaunders

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...]

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

July 31, 2011 | nsaunders

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 | nsaunders

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 | nsaunders

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 | 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...]

Syntax highlighting of R code at WordPress.com

May 20, 2011 | nsaunders

If your WordPress blog is hosted at WordPress.com (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 | nsaunders

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 | nsaunders

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 | nsaunders

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 | nsaunders

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 | nsaunders

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 ... [Read more...]

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Articles by nsaunders

Basic R: rows that contain the maximum value of a variable

Addendum to yesterday’s post on custom CSS and R Markdown

Custom CSS for HTML generated using RStudio

Twitter coverage of the ISMB 2012 meeting: some statistics

My day out at #osddmalaria

R gotcha for the week

Simple plots reveal interesting artifacts

A Friday round-up

Interacting with bioinformatics webservers using R

Popular topics at the BioStar Q&A site

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

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

Analysis of ISMB coverage at FriendFeed: 2008 – 2011

R: calculations involving months

Syntax highlighting of R code at WordPress.com

Friday fun with: Google Trends

Friday fun projects

R 2.12 to 2.13 package upgrade

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

The RStudio IDE: first impressions are positive

Articles by nsaunders

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