Amy D Willis

Wisdom from @titus.idyll.org on the final day of #STAMPS2025: "There's free as in beer, and there's free as in kittens. #Bioinformatics software is free as in kittens. You have to love and care for them or they... well... yeah."

The question was "...*on the same sequencing run*?"

Given that a Poisson regression with log link targets the same parameter as your NB regression, I'd be curious to see the coverage of robust Wald CI's. `rigr` wraps this, so does `raoBust`, so should be easy to add.

(Sorry -- I'm at a workshop today or I'd do it myself)

GitHub - statdivlab/raoBust: Generalized Linear Models with robust and non-robust Wald and Rao (score) tests Generalized Linear Models with robust and non-robust Wald and Rao (score) tests - statdivlab/raoBust

raoBust doesn't invert score tests @nlaroy.bsky.social, but it does implement (model-misspecification) robust score tests, which are amazing for inference.

Feel free to open a feature request. We'll see what we can do.

github.com/statdivlab/r...

The StatDivLab is getting excited for #STAMPS2025 and working on our lectures for 🤩 Stats Day 😻.

We ran this think-pair-share activity last year and, wow, the ensuing discussion was *very* engaged 😹😅

Reach out if you'd like to attend! Woods Hole, MA, July 14-24 2025. #microbiome #dataanalysis

Agreed that (eg) MAG assembly vs taxonomic estimation makes a huge difference to your answer. Also, please definitely read the Conflict of Interest statement for the shallow shotgun paper and note how much of its claims rely on bioinfomatic subsampling *and not actual shallow sequencing data*

Best workshop you can ever follow

That's wonderful to hear, Isabelle!! Thanks for sharing, too. Hope to see you there in 2026.

We had a last minute cancellation for STAMPS -- a phenomenal course on microbiome data analysis. Woods Hole, MA, July 14-24 2025.

If you or *anyone* you know is interested to attend, please email Titus &/or me... and we'll do what we can!!!

Thx for sharing widely! 🤞❤️

The StatDivLab is *fully* reliant on our NIGMS #MIRA R35 to bring you top-quality statistical methods for microbiome research. #NIH

They are quietly taking MIRAs away from this year's applicants. It's sneaky and scary.

Fight back! Call your reps and tell them to protect science!

It only takes 2 minutes to help defend our amazing program officers (and many other federal employees) and allow them to keep serving all Americans instead of responding to the whims of a single person

GitHub - statdivlab/radEmu Contribute to statdivlab/radEmu development by creating an account on GitHub.

How do I describe data with a lot of zeroes? Sparse.

How do I describe data with a lot of variance? High-variance.

How do I describe data where the totals convey complex information about an unknown quantity I care about? (abundance)

I don't. I just state my assumptions.

I hope you're all having a better week than me.

😽😽 7/6

I leave you with the StatDivLab mantra:

1. choose something meaningful to estimate
2. choose a sensible way to estimate it
3. choose tests that control Type 1 error

That's what we will keep doing, even if anonymous reviewers insist on buzzwords.

6/6

Saying "microbiome data is zero-inflated" leads people to seek out "zero-inflated models." Usually, these are bad methods with bad properties. Stay away. 5/6

Why does this matter? This sort of thinking leads biologists to trust estimators based on highly-parametrised parametric models that are (1) surely misspecified and (2) have terrible properties under misspecification. 4/6

Don't get me started on overdispersed, let alone compositional. Microbiome data is none of these, and I'm not new to this field. 3/6

In fact, if you look at blanks and other control data, you see a lot of incorrect detections. There's better evidence that microbiome data is NON-ZERO inflated than zero-inflated.

2/6

Please, #microbiome and #sequencing data are NOT zero-inflated. Let's stop repeating this nonsense. Zero-inflated compared to what?? Those zeroes carry important information about abundance and sequencing depth, and are not "inflated" in any sense. 1/6

The NIH budget is on a fast track to disaster An NIH insider explains what Republicans are likely to do next, and what we can do

How are DOGE & Trump planning to permanently decrease the NIH budget, and how do we fight back? -- by a courageous NIH whistleblower.

Thank you to this brave person for their clear analysis and constructive suggestions. #NIH #DOGE

donmoynihan.substack.com/p/the-nih-bu...

#EBAME 10 Microbial Ecogenomics Workshop! Brest🇫🇷, Oct 11-25, 2025.
A two-week workshop of lectures & tutorials to learn about omics data analysis for microbial ecology and evolution, all in the beautiful Brest Bay!
Apply here until June 1: maignienlab.gitlab.io/ebame

Please take 2 minutes to log that the ACA should be protected and expanded, and that trans healthcare is both the right thing to do and a great investment in Americans and America (or however you want to put it!) 💙💓🤍🤎🖤

absolutely!!!!!!! 🦤❤️🦠

A screenshot of the release notes for radEmu v2. Text available at https://github.com/statdivlab/radEmu/releases

We've just released radEmu v2.0.0 🥳🦤😻

`remotes::install_github("statdivlab/radEmu")`

A huge thanks to users for sharing their requests and questions, and to the maintenance team (Sarah and @davidandacat.bsky.social ) for their time and commitment!

Release notes: github.com/statdivlab/r...

Strategies and Techniques for Analyzing Microbial Population Structures (STAMPS) | Marine Biological Laboratory The STAMPS course promotes dialogue and the exchange of ideas between experts in environmental and microbiome analysis and offers interdisciplinary bioinformatics and statistical training to practitio...

Hello everyone, the STAMPS course on microbiome data analysis at @mblscience.bsky.social is open until Mar 11, 2025! Join us for a great experience!

Please ALSO check out my co-Director @amydwillis.bsky.social excellent post on how to write a great application: statdivlab.github.io/blog/article...

TL;DR:
✅ We care about whether you can benefit from the course
🥱(not how much you've already achieved)
😻Tell us about your data and what you want to learn!

I wrote a blog post about how to write a great #STAMPS2025 application!🙋❓🧑‍💻

Please share with anyone you know who is applying!!!! 🙏🤩

statdivlab.github.io/blog/article...

Thanks so much, Corey!!! Questions/comments welcome! 🙏🥳

Thanks to @naturemicrobiol.bsky.social for featuring our Comment in their Best Practices series, to the referees for constructive suggestions, and to @gibbological.bsky.social , @merenbey.bsky.social and Ting Ye for their excellent advice.

The latest from the StatDivLab -- guidance for your #microbiome data analysis with a focus on the #statistics. Planning, deciding, modeling, justifying, communicating, visualizing...

"Papers Need Friends" blog post coming shortly.