Amy D Willis
Biodiversity-loving, error bar-needing statistics nerd; Associate Professor @UWBiostat. Methods & software for #microbiome & #biodiversity data. She/her.
- I am delighted to share that the radEmu manuscript was accepted today to Biometrika 🥳 Sending gratitude to our users and reviewers for their enthusiasm and support!! Huge congrats to @davidandacat.bsky.social and Sarah Teichman on all their hard work and brilliance 😻❗ 1/
- Also, we made some common cases superdooper fast last week, so pull changes ⚡🏎️ Happy holidays, y'all! ❤️🦤❤️🦤❤️🦤❤️🦤❤️🦤❤️🦤❤️ 2/
- Oh yeah, ICYMI... radEmu is a method for differential abundance (or differential expression). It's especially well-suited to genomics and microbiome studies.
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View full threadDocumentation: statdivlab.github.io/radEmu/ Blog post: statdivlab.github.io/blog/article... 4/4
- ALDEx2's p-values are unusually strongly correlated with its effect sizes. Has anyone else noticed this? That... shouldn't happen. Data is actual shotgun coverages, ~8000 "taxa", 57 samples.
- I had this conversation again with someone today, so posting a screenshot of an old t**** for those who missed it the first time around -- or want a refresher! 1/n
- There's some more info on confounders in microbiome studies (and how they differ from precision variables) in this perspective we wrote last year: www.nature.com/articles/s41... 2/
- Same article but without the paywall (sorry, I didn't think they'd paywall it! duh Amy...) github.com/statdivlab/p... 3/
- Let's do better science together by using agreed-upon definitions! Woohoo! 4/4
- 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
- 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... ❤️❤️
- 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!
- 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 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
- Reposted by Amy D WillisBest workshop you can ever follow
- 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! 🤞❤️
- Reposted by Amy D WillisIt 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
- 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
- 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
- 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
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View full threadHow 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.
- 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...
- Reposted by Amy D Willis#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!) 💙💓🤍🤎🖤
- 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...
- Reposted by Amy D WillisHello 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...
- 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...
- 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!
- 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.
- A must-read for any microbiome researcher 🦠📐and a new addition to our #bestpractices series Planning and describing a microbiome data analysis by @amydwillis.bsky.social and @davidandacat.bsky.social www.nature.com/articles/s41...
- 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.
- Looking to improve your #microbiome data analyses skills? Hope to see you at #STAMPS2025 at @mblscience.bsky.social Applications Due: March 11, 2025 go.mbl.edu/STAMPS
- AND, I wrote a blog post about how to write a great application!🙋❓🧑💻 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! statdivlab.github.io/blog/article...
- First blog post! An overview and context of our work on distances between phylogenetic trees using BHV extension spaces statdivlab.github.io/blog/article...
