Andrew Severin

Yeah, well, it turns out grandma figured out all of the analysis methods for single-cell RNA-seq. 1/

snputils (snputils.org): A High-Performance Python Library for Genetic Variation and Population Structure biorxiv.org/content/10.648… 🧬💻🧪 github.com/AI-sandbox/snp…

kallisto sped up RNA-seq quantification by 50x. Now another 50x speedup... quantify hundreds of millions of reads in a few seconds. This seems too good to be true. But it's true! Incredible accomplishment by @pmelsted.

Here is the link to the repo: ↳ github.com/K-Dense-AI/cla…

Happy Holidays from the Iowa Soybean Research Center! conta.cc/4qi4wt9

Problem solving is by far the best part of being a manager of a bioinformatics core. I’ll be at PAG33 in San Diego this January. If you have an experiment you want to run by me or a tricky analysis you’re stuck on, let's meet up! 🧬 🖥️ #PAG33 Send me an gifhelp@iastate.edu

Genome annotation is an unsolved problem. Current tools struggle predicting gene models due to the limitations of short reads. With long read data, annotation will improve but still limited to RNA expression under many conditions. Function Annotation is similarly challenge #PAG33

The key to good project management adoption is a low barrier to entry. * Prepend folders with numbers 00_rawdata, 01_qc, etc * title, date, pwd, description, commands, results * Paired folders on Github with those on HPC cluster

Data analysis and discovery is the fun part but documentation is just as important if not more imporant in bioinformatics.. We use Github as our version controlled, searchable and sharable lab notebook to keep track of each project.

For example, you shouldn't use a splice-aware RNA-Seq aligner like STAR on reads from a prokaryotic organism. What other examples can you think of? 🧬 🖥️ #PAG33

Bioinformatics rests on three pillars of knowledge: Biology, Sequencing Technology and Software. Not understanding the assumptions and limitations of these pillars as they relate to your project will reduce your ability to explore your data. #PAG33

When I first started learning Unix commands, learning how to explore file contents was very important. Now that I teach bioinformatics, I came up with a fun way to remember these commands: A `cat` has a `head` and a `tail`, `more` or `less`. #PAG33 datascience.101workbook.org

gffutilsAI: An AI-Agent for Interactive Genomic Feature Exploration in GFF files biorxiv.org/content/10.648… 🧬🖥️🧪 github.com/ToyokoLabs/gff…

@jt_kerwin What made me disillusioned was how many different profs told me over years they knew this was a serious problem; nothing changed. If anything, it’s worse now. I realized any hopes of helping reform incentives in academia were as hopeless as me getting a job. That was a good bet.

Here's the link to the repo: github.com/Dicklesworthst…

How to finally break the “You’re absolutely right!” curse in ChatGPT

How to get ChatGPT to stop agreeing with everything you say:

I've recently discovered a really useful R package by Jan Broder Engler called tidyheatmaps. It's designed to make creating heatmaps from tidy data easy, especially for publication-quality visuals. The package uses pheatmap for detailed heatmaps with less coding. If you work with data like gene expression, you can get a heatmap set up quickly. The usage is straightforward, allowing for quick customization of your heatmaps. Check out the full guide for all options: jbengler.github.io/tidyheatmaps/ Give it a try for your next data visualization task. It could be a game changer for presenting your data. If you're interested in statistics, data science, and programming, you might also enjoy my free newsletter where such topics are covered regularly. More information: eepurl.com/gH6myT #Rpackage #DataScience #DataAnalytics #datastructure

OmniPath (omnipathdb.org): integrated knowledgebase for multi-omics analysis biorxiv.org/content/10.110… 🧬🖥️🧪 Python module github.com/saezlab/pypath R package github.com/saezlab/Omnipa… #Rstats

I'm up to 124 little mostly-vibe-coded apps on my tools.simonwillison.net site and most of them are trivial but some of them aren't, so I wrote up this guide to the ones I think are most worth checking out simonwillison.net/2025/Sep/4/hig…