👀 Absolute banger paper. Leveraging cattle/pig GWAS/eQTL to help explain the missing regulatory gap in humans. Consistent with previous works, selection makes identifying relevant eQTLs in humans challenging. www.biorxiv.org/content/10.6...

How I feel logging into a virtual machine, then ssh-ing into a cloud server, then connecting to an Rstudio server to access my data.

“Everything that scientists say hinges on the specifics of what they actually did. If you can’t (or don't) evaluate the details, you can’t evaluate the science. I'm grateful to the authors for providing access to those details.“

I have a SNP joke, but I don’t think you’d get the reference.

they can 100% amplify good judgment. You can put it to work on refactoring, testing, docs, debugging, product consistency, etc. But that requires _you_ to focus on it. And _that_ is hard.

🥇 The €100K Institutional Award goes to the Brazilian Reproducibility Initiative - a nationwide effort to evaluate lab biology research and the largest coordinated replication effort in the field worldwide, catalyzing lasting improvements across Brazil's research ecosystem. Congratulations!

"You've shown why we tell participants not to share their data online" ← So UK Biobank blame cohort members for their own re-identification? From just two quasi identifiers! This is victim-blaming in place of data governance. Yet again, serious questions need asking about UK Biobank governance.

One way we made it fast was by mapping with simpleaf (github.com/COMBINE-lab/...) 🥳 This gives a ~50x speed-up over CellRanger, and natively produces spliced vs unspliced reads. Percent spliced reads is IMO *the* most important QC metric for single nuclei data (link.springer.com/article/10.1...).

"Preprint servers are a time machine, they move everyone forward 12 months and speed up the exchange of ideas" ht @pedrobeltrao.bsky.social www.evocellnet.com/2021/06/a-no...

At this point I think my peer review has gotten to the point where I couldn't be replaced by an LLM, but I could be replaced with copy-and-paste 'The authors should add their statistical methods to the manuscript and carefully identify where and how they aggregate data'

I get contacted multiple times a week by users; it's really exciting to hear about all the cool science🌟 If {ukbrapR} supports your research, please cite it so I can track its impact (this really helps me!) Pro-tip: Use the {grateful} package to automatically include {ukbrapR} in your bibliography

I die a little every time I hear "oh I don’t use projects I just setwd()". Now that I voiced my concern to colleagues, I have to give a presentation on project-oriented workflows, I think it’s also a good time to introduce git. What’s your favorite teaching materials to get started? #rstats

New paper showing that much of the apparent success of protein language models in predicting mutational effects is a mirage: These models mostly memorize sites. 1/ www.biorxiv.org/content/10.6...

quarto-revealjs-editable has a new release with 5.0.0!! It is now much more stable, should now work everywhere, plus: - Rotation support - Undo/Redo - Copy qmd to Clipboard - keyboard controls github.com/EmilHvitfeld... #quarto

Issue 35 of #rdmweekly is out! Including: ➡️ Building Realistic Fake Datasets with Pointblank @richmeister.bsky.social ➡️ Rethinking TXT Files @kbriney.bsky.social ➡️ Economic Benefits of OS @plos.org ➡️ What Is Data Governance? @thegovlab.org and more! Link: rdmweekly.substack.com/p/rdm-weekly...

📢 New preprint out! tl;dr: Publish your code, add clear README's! 138 participants assessed data & code archiving practices across 1861 papers published at 7 @britishecologicalsociety.org journals, identified gaps & offered recommendations for improvement 🔗 doi.org/10.32942/X26...

"Dashboards" are very frustrating for exactly this reason. Needlessly fancy dashboards look impressive to people who don't use them.

OpenAI announces ChatGPT is now at the level of real scientific reviewers, “It just tells you to do single-cell RNAseq in response to every query” says Sam Altman

S4 methods developers when you type @ to access some slots. #rstats

Have you looked at the data? Me:

I feel like we could collectively come up with some great bond flick names re: #rstats, #GitHub, etc 😂 I submit for your approval: terrible ideas only. "MIT License to Kill" "Rebase Another Day" "The Dev Who Reviewed Me"

yes - there is certainly an uptick in fairly simple analyses. we've always had a policy excluding simple analyses (BLAST search etc) but what counts as simple is tricky to define and LLMs make a lot of things more simple to do... Others are seeing this too www.science.org/content/arti...

I mean, it's completely fine to say there's a 95% chance that a tibble will not behave as a data frame. (you can't deny that this was an epic example, incorporating baseR-tidyverse flamewar with frequentist-CI-interpretation-controversial)

Great to see this work out, led by Jon Rosen and co-supervised Karen Mohlke @klmohlke.bsky.social! Connecting to some recent threads here:

I wrote something. I hope it can be the start of more conversations about AI and the choices we all have to make. erincikanek.com/the-rumors-o...

Never change #rstats, never change

I just made an account and voted for this biology laboratory made of LEGO to "promote biological research and inspire more people into the world of biology". They need 10K votes. Reposting and/or voting below would be helpful. 🤗 beta.ideas.lego.com/product-idea...

This is (obviously) a step in the right direction: you should share all the code that led to the results (even if you think there is nothing "new" in your code). But who will review the code sharing?

> d3.js code with animations, but "vibe coding" scientific apps is likely to be very dangerous. I would need to completely gut this app of the backend stats functions and substitute my own.

I don’t know about living articles. But for computational work, I deeply appreciate the extended results/methods/discussions that end up buried in the supplementary figures. Sadly they get to live as static pdf when we could have much more engaging interactive formats.

For this week's #MemeMonday, don't be like Aragorn! If you're able to, please consider publishing your data in a reputable repository. We here at DRP deposit our rescued data in #DataLumos from @icpsr.bsky.social

Going through all the #rstats shitposting from the week-end

Wild and scary…

Improvements to methods should lead to more robust evidence and more rapid advances in knowledge. In their Perspective, Marcus Munafò & @mendelrandom.bsky.social look at why this hasn't been the case and what can be done about it #AcademicSky 🧪

How it feels picking an #rstats package to make tables

#bioinformatics #statistics #memes #bluesci

I wrote a blog for the Meta-Research Center expressing my infinite frustration about not getting data. What else is new, you might think? Well, I added an extra layer of annoyance directed at the journals who do NOTHING to enforce promised data sharing. metaresearch.nl/blog/2026/2/...

What does it take to succeed in science? Failure. Cambridge scientists from @labliston.bsky.social share the self-doubt behind their careers. Self-Doubt by Adrian Liston from @stcatharines.bsky.social and the Department of Pathology is Out tomorrow 👇 https://bit.ly/4a4tWUE #Careers #Science

I am deeply offended by boomerplyr (inspired by genzplyr), because I am NOT a boomer (squarely Xennial) and I "get" all the translations bradlindblad.github.io/boomerplyr/ #Rstats

every big data paper with a bold story that is impossible to comprehend, evaluate, and independently verify reminds me of DOPRA. i've come to increasingly appreciate small, unassuming papers with humble conclusions that you can track word for word, data point by data point, assumption by assumption.

New preprint alert: we use sign errors as a test of how well TWAS works. Very worryingly we find that TWAS gets the sign wrong around 1/3 of the time (compared to 50% for pure guessing). You can read more about our analysis here, and what we think is going on 👇

"We also find that approximately half of researchers never publish in a venue with an impact factor above 15, which, under journal-level evaluation regimes, may exclude them from consideration for opportunities. Many of these researchers publish equally influential work"

Remember: only YOU can prevent the zombie apocalypse

I wrote about missing heritability, "missing environmentality," and why I still think twin studies are interesting and valuable: kathrynpaigeharden.substack.com/p/twins-are-...