It’s plot recreation time! In this post, we’ll look at how we can recreate a plot in R. I thought it might be useful to provide the solution but also to detail the process I went through to get there. We have a FACS plot taken from a BD FACS Aria machine: Briefly, it’s a histogram of the fluorescence levels of 10000 cells from three different sources.
If you are into running, chances are that you will be chasing your PB (personal best) times. This post is about using R to search for your PBs, and to monitor them over time. Usually runners target four distances for PBs: 5 km, 10 km, half marathon and full marathon. It’s likely that a PB will come in a race of exactly that distance, but not necessarily. For example, you can hit a 5K PB during a 10K race.
The software that we use to do our work is our academic software stack . I often see requests for advice on which software works well. Since recommendations from labs that have road-tested a few options are quite valuable, I thought I would document what we’re currently using and why. I have tried to note if we’ve switched, tried alternatives and if we’re happy. The lab is Mac-based and we prefer FOSS solutions.
Giving effective feedback is a skill that, like any other, needs to be honed. I wouldn’t claim to be an expert but there are methods in how to give feedback that means that your guidance is more likely to help the person improve. Giving feedback to colleagues on grant applications is particularly tricky. It’s partly the high stakes involved: people’s livelihoods can be at stake and applicants’ best ideas are laid bare, so care is needed.
The Process_Folder template in Fiji is a wonderful thing. It’s the starting point of most of the ImageJ macros that we use in the lab. However, it has a problem. This post is about how to fix it. tl;dr use this gist instead of the built-in template. The Process_Folder template If you’re reading this, you probably know that the Process_Folder.ijm template is great.
As I write this, the moderation on major social media platforms has been degraded, and the tools available to the user to curate their feeds are quite poor. So how could we improve our science social media feeds?
How can we teach “R for cell biologists” rather than teaching R to cell biologists? I’ve noticed that many R training courses will teach R – regardless of who is taking the course – and leave it to the participants to figure out how they can use R in their own discipline.
Another year, another edition of “the papers I selected for a module that I teach”. Previous selections are grouped here or here. The list serves as a snapshot of interesting papers published in the previous 12 months or so. I hope it is useful to others who are looking for lists of papers to read, for student selections or for anything else.
It’s getting towards the end of the year so it is time to assemble a list of my favourite albums released in 2024. I have sporadically posted lists like this in the past. These twenty albums were the ones I liked the most (and the ones that I thought other people might like to hear). The Lemon Twigs – A Dream Is All We Know Genre: Power pop | [link] My favourite record of this year.
With the fervour of someone with an n = 1 positive experience, I thought I’d write about what I learned from a recent writing retreat. My University organises one-day events to encourage writing. They’re on-campus, in the neutral territory of the Library, so perhaps calling them “writing retreats” is a little far-fetched. Nonetheless, the idea is to provide a time and space for people to achieve some writing.
One of the joys of posting a preprint is seeing that people are viewing, downloading and (hopefully) reading your paper. On bioRxiv you can check out the statistics for your paper in the metrics tab. We posted a preprint recently and it clocked up over 1,000 views in the first day or so. This made me wonder: is that a lot of views or not? How does it compare to other preprints in our category?