David Rach

Superior batch alignment and hyper-dimensional cytometry representations allow ultra-sensitive classification of disease phenotypes
Andrews, T. D., Davies, A. R. et al.
Paper
Details
#UltraSensitiveDiseaseClassification #HyperDimensionalCytometry #BatchAlignmentInResearch

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!

How Quarto embed fixes data science storytelling | Emily Riederer Literate programming excels at capturing our stream of conscience. Our stream of conscience does not excel at explaining the impact of our work. Notebooks enable some of data scientists’ worst tendenc...

Technical writing is hard bcs "writing is thinking" but we often should tell our story not in the order we worked. Solution? I wrote a quick post on how @quarto.org 's embed shortcodes can reframe technical writing as reproducible evidence curation

www.emilyriederer.com/post/quarto-...

🧵 (1/n)

This is a bit of weird analysis - and looking through it I don’t necessarily recall seeing the same stuff. Fetal effector T cells are prone to death in vitro and there are relatively few in vivo. Most are treg (foxp3+) www.pnas.org/doi/10.1073/...

Grizzlies Were Raiding Montana Farms. Then Came Some Formidable Dogs.

www.nytimes.com/2025/07/22/c...

Reminders for researchers doing flow cytometry during the summer:

Hot weather can mess with your flow cytometry results. Keep an eye on the following:

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Importing Data with Python Importing data is a key step in the data science workflow. Here we compare data import for two key Python data-frame libraries - Polars and Pandas.

Importing data is a key step in the data science workflow. In our latest Python blog post, we compare this process for two key libraries - Polars and Pandas - emphasising how to convert to the correct data-type and why you should validate the structure and content of the imported data.

#rstats

Scientist’s cat, again, helps discover new virus - UF Health GAINESVILLE, Fla. — Pepper, the pet cat who made headlines last year for his role in the discovery of the first jeilongvirus found in the U.S., is at it again.…

Is Pepper co-author for providing the research material, or just mentioned in the acknowledgments? 🤔 #virus #virology #cat #immunosky

ufhealth.org/news/2025/sc...

Bioconductor: Planning a third decade of comprehensive support for genomic data science This opinion piece discusses the Bioconductor project for open-source bioinformatics and the engineering concepts underlying its effectiveness to date. Since the inception of Bioconductor in 2002 with...

www.cell.com/patterns/ful...

#bioconductor #rstats

Mark Walport begins conference by stating plainly that pre-pub peer review cannot reasonably be expected to assess quality of papers with 100 page supplements and terabytes of data

Hi bluesky! Here are new improvements to the flowcytometry app I made during my time in @elowitzlab.bsky.social. Now it supports exporting gated events as npy and mat. So you can gate data in your favorite graphic interface, then analyze them with python or Matlab! ym3141.github.io/EasyFlowQ/Ra...

Follow @econmaett.bsky.social, it's how I see most R things daily 😂 Also add the #rstats feed

New #rstats blog up!

solomonkurz.netlify.app/blog/2025-07...

This is the second post in the series where we use {brms} to learn {Stan} code. This time we review matrix notation, model matrices, and a new class of distribution functions in Stan.

ImmuneFM: Pre-training Foundation Model from Cytometry Data for Immunology Research

https://www.biorxiv.org/content/10.1101/2025.07.09.664020v1

GatingTree: Pathfinding Analysis of Group‐Specific Effects in Cytometry Data Advancements in cytometry technologies have led to a remarkable increase in the number of markers that can be analyzed simultaneously, presenting significant challenges in data analysis. Traditional ....

🚀 Our next-generation cytometry tool GatingTree now published in #CytometryPartA!
🔗 onlinelibrary.wiley.com/doi/10.1002/...

GatingTree enables systematic analysis of high-dimensional flow cytometry data, without relying on dimensionality reduction. 💻

Hexagonal logo for BioCAsia 2025 in Adelaide, featuring a stylized landscape with vineyards, mountains, a convention center, a grape cluster, and Bioconductor logo

📣 BioCAsia 2025: Call for Workshops

Join the Bioconductor stream at ABACBS 2025 in Adelaide!

Submit your hands-on workshop EOI by August 1.

Flexible 90-min blocks.

➡️ www.abacbs.org/abacbs-2025-...

#Bioconductor #BioCAsia2025 #RStats

Join the Bioconductor Developer Forum - R & Rust in Bioinformatics

🗓️ 28 July, 17:00–18:00 CEST

Discussing extendr, Rust packages, and real-world use cases.

🔗 blog.bioconductor.org/posts/2025-0...

#Bioconductor #RStats #RustLang #Bioinformatics

Projects BioHackathon Europe projects

💻🧬 Join the Bioconductor project at BioHackathon Europe 2025 (Berlin, Nov 3–7)!
In-person registration closes Tuesday, July 15
Project: github.com/elixir-europ...
#BioHackathon #Bioinformatics #Bioconductor

Parallel processing in purrr 1.1.0 The functional programming toolkit for R gains new capabilities for parallel processing and distributed computing using mirai.

#tidyverse purrr 1.1.0 is out - now with parallel processing!

Scale your #rstats map operations reliably and efficiently across multiple cores and even distributed systems.

Powered by the mirai framework, this unlocks new levels of performance.

Read more at:
www.tidyverse.org/blog/2025/07...

Which Kind of Science Reform What hope is there for science reform, if we can't agree on what to reform? Right now, principles are more important than practices.

How can we reform science? I have some ideas. But I am not sure you’ll like them, because they don’t promise much. elevanth.org/blog/2025/07...

A #flowcytometry, #rstats and #Stan pre-print! 😍

www.biorxiv.org/content/10.1...

I know the numbers are still rather small, but now do Positron!

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

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

ggplot2 4.0.0 is coming soon, and is moving some of the internals from S3 to the new S7 OOP system. This is worth a read if you're developing packages with ggplot2 (bioconductor or otherwise) blog.bioconductor.org/posts/2025-0... #Rstats

The Hunt for a 316-Year-Old Stradivarius Stolen in the Fog of War

www.nytimes.com/2025/07/06/a...

Bookmarking ☕ The BUV615 negative spill could probably still use some additional tinkering with brighter controls, doesn't look to be entirely UDS 🧐😂

Single Benzene Fluorophores: Elucidating the molecular structural origin of efficient emission across solid and solution phases
...joint paper with Jinsang Kim www.mse.engin.umich.edu/people/jinsang & Minsang Kwon kwonlab.snu.ac.kr

doi.org/10.1038/s414...

#compchemsky #chemsky #PiSky

It just happened again, as it happens multiple times each year: Someone's student asked me to look at their model output, I asked why they chose those variables, they say "these variables might influence outcome". This is a failure of training in biology, not student's fault. Committee is no better!

YouTube video by International Clinical Cytometry Society Tandem Dyes

🚀New Video Alert! Don't Miss It! 🚀
The ICCS Outreach Committee has released a new video on tandem dyes in flow cytometry. More videos coming soon, so please *subscribe* to our YouTube channel so you don't miss any!
Watch it now at www.youtube.com/watch?v=5cV7...
#PathSky #Flowcytometry #Hemepath

.... LibreOffice it is then ....