Blog Archives

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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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

Read more »

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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Project Tycho, ggplot2 and the shameless stealing of blog ideas

April 14, 2015
By
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

Read more »

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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Configuring the R BatchJobs package for Torque batch queues

March 31, 2015
By
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

Read more »

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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PubMed retraction reporting update

March 23, 2015
By
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

Read more »

PMRetract: PubMed retraction reporting rewritten as an interactive RMarkdown document

March 22, 2015
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PMRetract: PubMed retraction reporting rewritten as an interactive RMarkdown document

Back in 2010, I wrote a web application called PMRetract to monitor retraction notices in the PubMed database. It was written primarily as a way for me to explore some technologies: the Ruby web framework Sinatra, MongoDB (hosted at MongoHQ, now Compose) and Heroku, where the app was hosted. I automated the update process using

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