Blog Archives

Evidence for a limit to effective peer review

December 18, 2016
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Evidence for a limit to effective peer review

I missed it first time around but apparently, back in October, Nature published a somewhat-controversial article: Evidence for a limit to human lifespan. It came to my attention in a recent tweet: Just wow https://t.co/fupXIOAC43 pic.twitter.com/vsxT3VyTg6 — Nick Loman (@pathogenomenick) December 11, 2016 The source: a fact-check article from Dutch news organisation NRC titled “Nature

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An Analysis of Contributions to PubMed Commons

December 1, 2016
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An Analysis of Contributions to PubMed Commons

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 analyse PubMed Commons data. The

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Putting data on maps using R: easier than ever

November 23, 2016
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Putting data on maps using R: easier than ever

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 couple of key R packages in this

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The y-axis: to zero or not to zero

November 20, 2016
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The y-axis: to zero or not to zero

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 out. pic.twitter.com/wby3gta26m — D Yanagizawa-Drott (@yanagiz) November 9,

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Let’s (briefly) revisit the Nobel API

October 9, 2016
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Let’s (briefly) revisit the Nobel API

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, it’s all old white men” chart

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Novelty: an update

October 21, 2015
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Novelty: an update

A recent tweet: @neilfws I enjoyed this: https://t.co/ynyHRbgpLN 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 to

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R and the Nobel Prize API

October 20, 2015
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R and the Nobel Prize API

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 an API. I’ve published a

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Searching for duplicate resource names in PMC article titles

September 16, 2015
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Searching for duplicate resource names in PMC article titles

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 pattern. There may even be

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Analysis of gene expression timecourse data using maSigPro

May 28, 2015
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Analysis of gene expression timecourse data using maSigPro

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 worked with timecourse data before,

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Searching for the Steamer retroelement in the ocean metagenome

May 25, 2015
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Searching for the Steamer retroelement in the ocean metagenome

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 data from ocean metagenomics

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