Publications by Stephen Turner
PLANES: Plausibility Analysis of Epidemiological Signals
This blog has moved. This is reposted from Paired Ends:https://blog.stephenturner.us/p/planes-plausibility-analysis-of-epidemiological-signals-rplanes-r-package PLANES provides a set of methods for evaluating the plausibility of epidemiological signals and forecasts. The PLANES methods are available in the rplanes R package and Shiny app.Motivatio...
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biorecap: an R package for summarizing bioRxiv preprints with a local LLM
This is re-posted from my newsletter, where I’ll be posting from now on:https://blog.stephenturner.us/p/biorecap-r-package-for-summarizing-biorxiv-preprints-local-llm—TL;DRI wrote an R package that summarizes recent bioRxiv preprints using a locally running LLM via Ollama+ollamar, and produces a summary HTML report from a parameterized RMarkdow...
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Use R to prompt a local LLM with ollamar
This is reposted from the original article: https://blog.stephenturner.us/p/use-r-to-prompt-a-local-llm-withUse R to prompt a local LLM with ollamar: Using R to prompt llama3.1:70b running on my laptop with Ollama + ollamar to tell me what’s interesting about a set of genes, and to summarize recent bioRxiv preprintsSubscribe at https://blog.step...
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Moving to blog.stephenturner.us (Paired Ends)
My new blog/newsletter (“Paired Ends”) is now at blog.stephenturner.us. I’ll be posting semi-regular updates and literature highlights in bioinformatics, computational biology, and data science, along with the occasional post on programming. Head over to blog.stephenturner.us to subscribe by email, or add the RSS feed to your favorite read...
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Use meaningful color schemes in your figures
Some of the best figure design ideas come from cartographers. If you’ve ever read a Tufte book you’ve seen lots of examples. Let’s talk about using color effectively. Penn State geography professor Cindy Brewer’s ColorBrewer tool for selecting color schemes for figures has been conveniently packaged into an R library called R...
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Side by side analyses in Stata, SPSS, SAS, and R
I’ve linked to UCLA’s stat computing resources once before on a previous post about choosing the right analysis for the questions your asking and the data types you have. Here’s another section of the same website that has code to run an identical analysis in all of these statistical packages, with examples to walk through (as ...
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NYT: In Simulation Work, the Demand Is Real
The New York Times published this interesting article on how the ability to design and perform computer simulations is a highly marketable skill for careers across many disciplines.In methodology development we use simulation nearly every day. We’ve developed our own specialized genetic data simulation software, genomeSIMLA, that�...
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PDF tutorial from R course (Introduction to R)
Writing from the previously mentioned intro to R course at the Kennedy Center. If you couldn’t make it you can download all the course materials from Theresa Scott’s website, under the “Current Teaching Material” heading. Here is a direct link to the PDF for the overview materials that we’re going over today, along with th...
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Weekly R Clinic
For readers at Vanderbilt: At yesterday’s R course I found out that Theresa Scott in the Biostatistics department holds a weekly R clinic and encourages new R users who want to learn more to bring any questions about R, or even your own code and data. The R clinic is held weekly on Thursday from 2:00-3:00 in MCN. You can find her ...
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Getting help with R
There’s no doubt that by now you’ve noticed that we’re big fans of R around here. It’s completely free, has superior graphing capabilities, and with all the extension packages available there isn’t much it can’t do. One of the problems with R especially to new users is that it isn’t obvious how to find help when you ne...
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