Susan Holmes🎲🖥️🧬

An R package for working with generalized additive models Graceful 'ggplot'-based graphics and utility functions for working with generalized additive models (GAMs) fitted using the 'mgcv' package.

🚀 gratia 0.11.0 is out!

Now has a paper in JOSS — please cite 📄 doi.org/10.21105/jos...

Experimental parallel processing ⚡

New assemble() for building plots 🎨

Better support for complex families + new diagnostics 🧪

Lots of bug fixes + polish ✨

👉 gavinsimpson.github.io/gratia/

#Rstats

This photo captures a striking piece of urban street art on the side of a weathered yellow building by the artist Bordalo II. The artwork is a massive, three-dimensional mural of a rabbit, created using a combination of colorful paint and recycled materials such as scrap metal, plastic, and wood. The textures and objects give the rabbit a layered, sculptural quality that makes it appear to leap out from the wall. The building itself shows signs of age, with peeling paint and cracks, adding a sense of history and contrast to the vibrant modern artwork. A small cobblestone street runs alongside, lined with older buildings painted in muted tones, one with red doors and another in pale yellow. A car is parked further down the street, and traffic signs are visible — a "no entry" sign on the right wall and a "no parking" sign on the left near the artwork. Overhead, the sky is a brilliant clear blue, providing a vivid backdrop that enhances the bright colors of the mural.

#Pieces of Trash

2025
Porto, Portugal 📍
Artwork by Bordalo II

#portugal #porto #Gaia #rabbit #Bunny #dourovalley #visitportugal #travel #oporto #portoportugal #visitporto #streetart #portuguese #winelovers #ButroTravel #streetphotography #urbanphotography #BlueSkyArtShow

Quarto website displaying a link to the inactive @quarto_pub Twitter account.

Hey @quarto.org since you're no longer posting on x.com/quarto_pub how about adding a link to your bluesky profile to quarto.org? 🦋
#rstats #pydata @posit.co

My lab is going to be imminently looking for a computer scientist or a biologist with deep understanding of R to develop and give bioinformatic education to postdocs. This is perfect for someone who likes teaching. You'd need to be in the Pittsburgh area. Feel free to reach out with questions.

I wrote this talk with an LLM - Hadley Wickham (useR! 2025 Keynote 1) YouTube video by Duke Center for Computational Thinking

www.youtube.com/live/ctc2kx3...

The Journal of Open Source Software (@joss-openjournals.bsky.social‬) is looking for editors. Come join our team!

I've only been an editor for a few months, but I love working with JOSS. Our peer review process is actually collaborative, and we're Diamond Open Access.

#AcademicSky 🧪 ⚗️ #CompChem

The President of United States firing the commissioner of the statistics bureau because the unemployment numbers are not good reminds me of that classic Stalin moment, executing the statisticians because they reported too many deaths the 1937 census

www.jstor.org/stable/2639947

Je peux même faire aussi un #beamer pour une présentation directement dans #Rstudio avec #quarto, c'est troooop bien !

Prochain obj si j'y arrive : une appli R shiny sur un beamer 🙂

Having a boy or girl at birth is a coin toss: Reanalyzing a new study. – Marcos Huerta Data is Singular

The paper in Science Advances that said some moms have more boys than girls that got a lot of press attention? I dove into their raw data and their conclusions seem flawed. #dataBS

marcoshuerta.com/posts/baby-b...

GitHub - flatironinstitute/stan-playground: Run Stan models in the browser Run Stan models in the browser. Contribute to flatironinstitute/stan-playground development by creating an account on GitHub.

💻 This was also my first time using Stan playground (github.com/flatironinst...) to teach a class! Thank you Brian Ward for creating this tool and helping me set it up for the class!

Posting on bioRxiv counts.

Chevreul: an R bioconductor package for exploratory analysis of full-length single cell sequencing. #SingleCell #scRNAseq #FullLengthRNA #GigaByte
gigabytejournal.com/articles/158

Post-Doc Researcher for the evaluation of external influences on blood proteomics and metabolomics data Eurac Research · Bozen/Bolzano

Interested in a #PostDoc / researcher position in my team at Eurac Research 🇮🇹?

👉 apply if you like

- analyzing large-scale #proteomics and #metabolomics data
- #rstats and/or #Python
- reproducible research
- hiking ⛰️ (on weekends!)

🔗 eurac.onboard.org/jobs/Q4301nGV

Bioconductor and ggplot2 4.0.0: What’s Changing and How to Prepare – Bioconductor community blog Preparing for the upcoming update - key changes, potential breakages, and what developers and users can do

📝 New blog post: Bioconductor and ggplot2 4.0.0 - What’s Changing and How to Prepare

A major ggplot2 update is coming and may impact Bioconductor packages. What’s changing, how to test, and where to get help 👉 blog.bioconductor.org/posts/2025-0...

#Bioconductor #RStats

A new mural has been unveiled in the French city of Roubaix to mark #July4th.

(🎨 Judith de Leeuw)

Fellowships, grants and career support – Postdoctoral Fellowships – EMBO Supporting internationally mobile postdoctoral researchers in Europe and around the world

Looking for a #LifeSciences postdoctoral #opportunity? 🧪 Have a look at the EMBO Postdoctoral Fellowships for internationally mobile scientists in #Europe and globally.

Apply before 11 July: www.embo.org/funding/fell...
#research #funding #postdoc

RaukR is an #rstats summer school (~1.5 weeks) I've taught at a few times. Highly recommended for content (of course I'm biased 😁), smooth organization, and an amazing location (Visby 🏰 on the island of Gotland in Sweden 🇸🇪). Intrigued? Sign up to get notified when RaukR 2026 opens for registration.

Model Context Protocol Server For Your R Sessions Implements a model context protocol (MCP) server for your R sessions, allowing MCP-compatible apps like Claude Desktop and Claude Code to run R code in your active R sessions in order to better answer...

For the early adopters of acquaint, a package implementing the Model Context Protocol in #rstats: the package has been renamed to mcptools and no longer exports btw's tools by default.

See the package website for more info posit-dev.github.io/mcptools/

Love this CoFest energy!
Great to see Galaxy and Bioconductor developers working side-by-side at #GBCC2025, exploring, coding, and learning from each other 💻💙

@galaxyproject.bsky.social @bioconductor.bsky.social

Please watch one of the best pieces of television ever made. RIP Ricky Jay

Just published in JOSS: '<code>medRCT</code>: Causal mediation analysis estimating interventional effects mapped to a target trial in R' https://doi.org/10.21105/joss.08063

📢 Poster 1001 at #MetSoc2025: Marilyn De Graeve on our #SpectriPy #rstats package to integrate #python and #rstats packages for #MassSpec data analysis . TODAY

New expanded @hipcproject.bsky.social starter pack: go.bsky.app/AozZWPx

EuroBioC2025 late-breaking poster abstract submission Please fill the form below before the end of Friday July 11th, 2025, to submit an abstract for a poster to be considered for presentation at EuroBioC2025 in Barcelona on September 17-19, 2025…

📣 Late-breaking poster call for #EuroBioC2025 is now open!

Submit by July 11 to present your work in Barcelona this September.
🔗 forms.gle/ewTGdKzB2xyE...
📅 Notifications by July 15

#Bioconductor #Bioinformatics

Screen of speaker saying “Sorry that I can’t be there”

After lunch: Wolfgang Huber (online) with: Single cell differential expression without discrete cell types

Can we replace +/- cell type characterization with a continuous parameterization?

Susan and I wrote a book together: www.huber.embl.de/msmb/ Modern Statistics for Modern Biology

🌸 This morning in Ponte de Lima, the streets are adorned with flower carpets ephemeral works of art lovingly created by locals for the Corpus Christi procession (4:30 PM).
A unique moment of tradition, art, and faith not to be missed! 📸 #TapetesFloridos #PontedeLima #CorpoDeDeus #Portugal

Guidelines for preventing and reporting contamination in low-biomass microbiome studies Nature Microbiology - In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize...

Hope this is useful - consensus statement "Guidelines for preventing and reporting contamination in low-biomass microbiome studies" rdcu.be/er3Io

Yes, that's why he is seen as the inventor of EDA, where the graphics were made by the data scientist themselves to see what was going on and were not for the final publication, but visualization as exploration...

#Statsky 💻

Please pass along - postdoc position! with our working group on #FunctionalTraits and rarity. This is part of the FREE (Functional Rarity in Ecology and Evolution) working group led by Cyrille Violle in Montpellier France 🧪🌐🌾 emploi.cnrs.fr/Offres/CDD/U...