Remember the “AI rat penis” incident at Frontiers in Cell & Developmental Biology? Well, that was two and a half years ago. That’s enough water under the bridge to now check in and see how this incident affected the journal. If we look at how many papers published, we should be able to see whether […]
How can we make microscopy images accessible to everyone, including those who have colour deficiencies in vision? I’ve written previously about a tool to check figures for accessibility. There is also helpful guidance out there (and here). With increased awareness around this issue, I’ve noticed that these days referees are more likely to request changes […]
Niche tips are the bedrock of quantixed. Here is another. Posted purely because we reran into this problem and had to refigure out the answer. Problem We have a segmented image. Each object has a unique integer assigned as a pixel value. How do we get a list of the integers corresponding to the objects? […]
This is a short post to announce the release of an R package, VolcanoPlotR. Background Using proteomics, we often want to compare two experimental groups. A popular way to visualise this comparison this is via a volcano plot, where the enrichment of proteins in one condition is towards the right and their de-enrichment (or their […]
A chance comment from a colleague led to today’s post. Competition for research grants in the UK has become more intense recently. Success rates have dropped, and this has been attributed to more applications, against a backdrop of a flat investment in science by the government. My colleague thought that the cost of each proposal […]
I wanted to know: After a little bit of searching, I couldn’t find any answers. So I decided to use R to retrieve the necessary info from Uniprot and calculate it myself. I thought I’d post it here in case it’s useful for others. Human We’ll start with the info I wanted. According to Uniprot […]
It’s often the way. I posted recently about how to pace a marathon and very quickly received feedback that would’ve improved the original post. Oh well, no going back. This is take two. So, we have a dataset of all runners from the 2025 New York City Marathon. We want to know how should you […]
I’ve posted about publication lag times previously. The “lag” refers to the time from submitting a paper and it appearing in a journal. Publication lag times are still a frustration for researchers. Although preprints circumvent the delay in sharing science with others, publication is still king when it comes to evaluation. Contracts are short and […]
How does the average marathoner pace their race? In this post, we’ll use R to have a look at a large dataset of marathon times to try to answer this question. The ideal strategy would be to “even split” the race. This is where you run continually at the same pace from kilometre 0 to […]
In a previous post, I described how to run a session to teach R to cell biologists. In this post we’ll look in a bit more detail at one of the steps: how to load data into R. As a reminder, a typical analysis task in cell biology follows these steps: Loading data into R […]