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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R and the Nobel Prize API

October 20, 2015
By
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

Read more »

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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Searching for duplicate resource names in PMC article titles

September 16, 2015
By
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

Read more »

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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Analysis of gene expression timecourse data using maSigPro

May 28, 2015
By
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,

Read more »

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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Searching for the Steamer retroelement in the ocean metagenome

May 25, 2015
By
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

Read more »

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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