Blog Archives

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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Some basics of biomaRt

April 27, 2015
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Some basics of biomaRt

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 “the answer is BioMart” (there

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R 3.1 -> 3.2 upgrade notes

April 19, 2015
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R 3.1 -> 3.2 upgrade notes

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 rJava

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Project Tycho, ggplot2 and the shameless stealing of blog ideas

April 14, 2015
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Project Tycho, ggplot2 and the shameless stealing of blog ideas

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 R graphics

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Configuring the R BatchJobs package for Torque batch queues

March 31, 2015
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Configuring the R BatchJobs package for Torque batch queues

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 system to allocate nodes

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PubMed retraction reporting update

March 23, 2015
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PubMed retraction reporting update

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. That becomes (100

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