This week’s recap highlights PhyloSketch for interactively drawing and manipulating phylogenies, Uncalled4 for nanopore DNA and RNA modification detection, Severus for SV calling from long reads, CREsted for modeling synthetic cell type-specific enhancers, and a review on transformers and genome language models.
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.
Reposted from the original at: https://blog.stephenturner.us/p/r-production-ai ... Python isn't the only game in town anymore: R can interact with local and cloud LLM APIs, inspect and modify your local R environment and files, implement RAG, computer vision, NLP, evals, &
There was a time in late 2023 to early 2024 when I and probably many others in the R community felt like R was falling woefully behind Python in tooling for development using AI and LLMs. This is no longer the case. The R community, and Posit in particular, have been on an absolute tear bringing new packages online to take advantage of all the capabilities that LLMs provide.
Data Sustainability In the rapidly evolving landscape of bioinformatics, research data is the bedrock of discovery, innovation, and progress. But how secure is this foundation for the future?
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.
This week’s recap highlights polars-bio for fast and scalable and out-of-core operations on large genomic interval datasets, combining DNA and protein alignments to improve genome annotation with LiftOn, feature selection methods for scRNA-seq, STRkit for read-level genotyping of short tandem repeats using long reads and single-nucleotide variation, and nf-core/detaxizer for decontamination of human sequences in metagenomics data.
BOSC 2025 keynote speakers and panelists KEYNOTE: Chris Mungall Open Knowledge Bases in the Age of Generative AI KEYNOTE: Christine Orengo Working together to develop, promote and protect our data resources: Lessons learnt developing CATH and TED Panel: Data Sustainability BOSC 2025 Schedule at a Glance Schedule of talks coming soon! Poster list coming soon!
Reposted from the original at https://blog.stephenturner.us/p/quarto-books. ...In the spirit of learning in public, I wanted an excuse to dive into Quarto to learn more about publishing formats beyond simple PDF and HTML documents.If you’re not familiar, Quarto (quarto.org) is the successor to RMarkdown, the next-generation scientific publishing system that works natively with Python, R, and OJS.
In the spirit of learning in public, I wanted an excuse to dive into Quarto to learn more about publishing formats beyond simple PDF and HTML documents. If you’re not familiar, Quarto (quarto.org) is the successor to RMarkdown, the next-generation scientific publishing system that works natively with Python, R, and OJS. If you already have RMarkdown you probably don’t have to do anything to it to get it to render with Quarto.
This week’s recap highlights compendium of human gene functions derived from evolutionary modelling from the Gene Ontology Consortium, an AI reasoning model applied to rare disease diagnosis, an agentic AI for scRNA-seq data exploration, and applying FAIR principles to scientific workflows.