Publications by nsaunders
Box plots. Like box plots, only…box plots.
On a rare, brief holiday (here and here, if you’re interested; both highly-recommended), I make the mistake of checking my Twitter feed: paging @neilfws . . . RT @psudmant: Ground breaking new methods from @naturemethods – boxplots – no rly nature.com/nmeth/journal/…— Chris Miller (@chrisamiller) January 30, 2014 This points me to BoxP...
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A minor update to my “apply functions” post
One of my more popular posts is A brief introduction to “apply” in R. Come August, it will be four years old. Technology moves on, old blog posts do not. So: thanks to BioStar user zx8754 for pointing me to this Stack Overflow post, in which someone complains that the code in the post does not work as described. The by example is now fixed. S...
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This is why code written by scientists gets ugly
There’s a lot of discussion around why code written by self-taught “scientist programmers” rarely follows what a trained computer scientist would consider “best practice”. Here’s a recent post on the topic. One answer: we begin with exploratory data analysis and never get around to cleaning it up. An example. For some reason, a resear...
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Converting a spreadsheet of SMILES: my first OSM contribution
I’ve long admired the work of the Open Source Malaria Project. Unfortunately time and “day job” constraints prevent me from being as involved as I’d like. So: I was happy to make a small contribution recently in response to this request for help: Can anyone help @O_S_M to convert this spreadsheet ( malaria.ourexperiment.org/biological_dat...
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When life gives you coloured cells, make categories
Let’s start by making one thing clear. Using coloured cells in Excel to encode different categories of data is wrong. Next time colleagues explain excitedly how “green equals normal and red = tumour”, you must explain that (1) they have sinned and (2) what they meant to do was add a column containing the words “normal” and “tumour”....
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Venn figures go wrong
6-way Venn bananaI thought nothing could top the classic “6-way Venn banana”, featured in The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. That is until I saw Figure 3 from Compact genome of the Antarctic midge is likely an adaptation to an extreme environment.5-way Venn roadkill What’s odd is that Figure 2 i...
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Ebola, Wikipedia and data janitors
Sometimes, several strands of thought come together in one place. For me right now, it’s the Wikipedia page “Ebola virus epidemic in West Africa”, which got me thinking about the perennial topic of “data wrangling”, how best to provide public data and why I can’t shake my irritation with the term “data science”. Not to mention Ebo...
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PubMed Publication Date: what is it, exactly?
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. library(rentrez) es <- entrez_search("pubmed", ""Retracted Publication"[PTYP] 2013[PDAT]", usehistory = "y") es$count # [1] 117 117 articles....
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Bioinformatics journals: time from submission to acceptance, revisited
Before we start: yes, we’ve been here before. There was the Biostars question “Calculating Time From Submission To Publication / Degree Of Burden In Submitting A Paper.” That gave rise to Pierre’s excellent blog post and code + data on Figshare. So why are we here again? 1. It’s been a couple of years. 2. This is the R (+ Ruby) version....
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Counting things is hard for a given value of “things”
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 expect rebuttals from people like Michael Eisen and ...
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