Amy D Willis

With much gratitude to everyone who supported the wonderful #STAMPS summer course at the MBL, I share that STAMPS will not be offered in 2026.

💔😿

pixi is awesome. That is all.

@titus.idyll.org you're all over this, right?

Are you looking for a #tenuretrack or #openrank job in #biostatistics or #statistics? @fredhutch.org is hiring! Seattle is a wonderful place to grow your career; the bio/stat & science scene here is world-class; and you will work w/ amazing UW Biostat students. Apply!
apply.interfolio.com/176402

dude you can just text me with this stuff ❤️

% of microbiome (& changes) aren't identifiable from HTS, but stacked barplots are helpful for generating clues esp if big shifts

data snooping has implications for error rate control. there isn't a hypothesis you're interested in?

good luck & enjoy xx

A screenshot of the header for the tutorial linked in the post

In other news, I just had the great pleasure of teaching at #EBAME10 in Brittany 🇫🇷🥐.

For this workshop, I made a tutorial showing how to use radEmu with the taxonomic profiling output of #anvio 😍😻

Workflow available for everyone on our blog: statdivlab.github.io/blog/article...

❤️❤️

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

Happy Friday from the StatDivLab!

We just made updates to radEmu to make it faster & more stable than ever.

Thanks to all our users -- we're excited to keep supporting it.

github.com/statdivlab/r...

Interpretable and robust microbial differential abundance, woohoo!

Thanks for your interest, @genomesevolve.bsky.social ! As a field, *on average*, I feel we have moved...

1. away from obsessing over alpha and beta diversity comparisons
2. towards comparisons that are less sensitive to rare/undetected species (than diversity)

So 📈

🥳

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!!!!!!! 🦤❤️🦠