Articles by nsaunders

An Analysis of Contributions to PubMed Commons

December 1, 2016 | 0 Comments

I recently saw a tweet floating by which included a link to some recent statistics from PubMed Commons, the NCBI service for commenting on scientific articles in PubMed. Perhaps it was this post at their blog. So I thought now would be a good time to write some code to ...
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Putting data on maps using R: easier than ever

November 23, 2016 | 0 Comments

Using R to add data to maps has been pretty straightforward for a few years now. That said, it seems easier than ever to do things like use map APIs (e.g. Google, Open Street Map), overlay quite complex data visualisations (e.g. “heatmap-style” densities) and even generate animations. A ...
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The y-axis: to zero or not to zero

November 20, 2016 | 0 Comments

I don’t “do politics” at this blog, but I’m always happy to do charts. Here’s one that’s been doing the rounds on Twitter recently: A quick look at turnout data: It seems 2016 was nothing special for the Rep-candidate. It's the Dem-candidate that didn't get the vote ...
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Let’s (briefly) revisit the Nobel API

October 9, 2016 | 0 Comments

It’s always nice when 12-month old code runs without a hitch. Not sure why this did not become a Github repo first time around, but now it is: my RMarkdown code to generate a report using data from the Nobel Prize API. Now you too can generate a “gee, ...
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Novelty: an update

October 21, 2015 | 0 Comments

A recent tweet: @neilfws I enjoyed this: Have you published (or are you thinking about publishing) this analysis anywhere? — Marcus Munafo (@MarcusMunafo) October 7, 2015 made me think (1) has it really been 5 years, (2) gee, my ggplot skills were dreadful back then and (3) did I really not know how ...
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R and the Nobel Prize API

October 20, 2015 | 0 Comments

The Nobel Prizes. Love them? Hate them? Are they still relevant, meaningful? Go on admit it, you always imagined you would win one day. Whatever you think of them, the 2015 results are in. What’s more, the good people of the Nobel Foundation offer us free access to data via ...
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Searching for duplicate resource names in PMC article titles

September 16, 2015 | 0 Comments

I enjoyed this article by Keith Bradnam, and the associated tweets, on the problem of duplicated names for bioinformatics software. I figured that to some degree at least, we should be able to search for such instances, since the titles of published articles that describe software often follow a particular ...
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Analysis of gene expression timecourse data using maSigPro

May 28, 2015 | 0 Comments

About a year ago, I did a little work on a very interesting project which was trying to identify blood-based biomarkers for the early detection of stroke. The data included gene expression measurements using microarrays at various time points after the onset of ischemia (reduced blood supply). I had not ...
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Searching for the Steamer retroelement in the ocean metagenome

May 25, 2015 | 0 Comments

Last week, I was listening to episode 337 of the podcast This Week in Virology. It concerned a retrovirus-like sequence element named Steamer, which is associated with a transmissible leukaemia in soft shell clams. At one point the host and guests discussed the idea of searching for Steamer-like sequences in the ...
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Some basics of biomaRt

April 27, 2015 | 0 Comments

One of the commonest bioinformatics questions, at Biostars and elsewhere, takes the form: “I have a list of identifiers (X); I want to relate them to a second set of identifiers (Y)”. HGNC gene symbols to Ensembl Gene IDs, for example. When this occurs I have been known to tweet “...
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R 3.1 -> 3.2 upgrade notes

April 19, 2015 | 0 Comments

My machines upgraded from R version 3.1.3 to version 3.2.0 last week, which means that existing code suddenly cannot find packages and so fails. Some notes to myself, possibly useful to others, for what to do when this happens. Relevant to Ubuntu-based systems (I use Linux Mint). 1. Update packages 1.1. rJava issues My ...
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Project Tycho, ggplot2 and the shameless stealing of blog ideas

April 14, 2015 | 0 Comments

Last week, Mick Watson posted a terrific article on using R to recreate the visualizations in this WSJ article on the impact of vaccination. Someone beat me to the obvious joke. @BioMickWatson @pathogenomenick Nice quilt plot. — Ed Yong (@edyong209) April 9, 2015 Someone also beat me to the standard response whenever base ...
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Configuring the R BatchJobs package for Torque batch queues

March 31, 2015 | 0 Comments

I was asked recently to look at some R code which performs “embarrassingly parallel” computations (the same function, multiple times, different parameters) and see whether I could modify it to run on one of our high-performance computing clusters. The machine has 63 virtual compute nodes and uses the TORQUE batch queue ...
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PubMed retraction reporting update

March 23, 2015 | 0 Comments

Just a quick update to the previous post. At the helpful suggestion of Steve Royle, I’ve added a new section to the report which attempts to normalise retractions by journal. So for example, J. Biol. Chem. has (as of now) 94 retracted articles and in total 170 842 publications indexed in PubMed. ...
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Just how many retracted articles are there in PubMed anyway?

March 19, 2015 | 0 Comments

I am forever returning to PubMed data, downloaded as XML, trying to extract information from it and becoming deeply confused in the process. Take the seemingly-simple question “how many retracted articles are there in PubMed?” Well, one way is to search for records with the publication type “Retracted Article”. As ...
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Make prettier documents by reusing chunks in RMarkdown

February 23, 2015 | 0 Comments

No revelations here, just a little R tip for generating more readable documents. There are times when I want to show code in a document, but I don’t want it to be the first thing that people see. What I want to see first is the output from that ...
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Counting things is hard for a given value of “things”

December 1, 2014 | 0 Comments

This post is just a summary of some interesting online discussion from last week around open access publishing. I learned a few things about definitions and PubMed/PMC filters. It all begins with an opinion piece, “Open access is tiring out peer reviewers.” With a title like that you might ...
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PubMed Publication Date: what is it, exactly?

September 23, 2014 | 0 Comments

File this one under “has troubled me (and others) for some years now, let’s try to resolve it.” Let’s use the excellent R/rentrez package to search PubMed for articles that were retracted in 2013. 117 articles. Now let’s fetch the records in XML format. Next question: which XML ... [Read more...]
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