How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3) doi.org/10.1038/s415...

Analysis of multi-condition single-cell data with latent embedding multivariate regression - Nature Genetics

Latent embedding multivariate regression models multi-condition single-cell RNA-seq using a continuous latent space, enabling data integration, per-cell gene expression prediction and clustering-free ...

doi.org

When NOT to use DESeq2 for RNA-seq analysis? DESeq2 is the gold standard for bulk RNA-seq, but it has limitations. If you’re analyzing large datasets, beware of inflated false discovery rates (FDR). 🧵👇

2/ But here’s the issue: When you have hundreds of samples, DESeq2’s FDR can increase significantly. A 2022 study highlights this problem:genomebiology.biomedcentral.com/articles/10... genomebiology.biomedcentral.com/articles/10...

Exaggerated false positives by popular differential expression methods when analyzing human population samples - Genome Biology

When identifying differentially expressed genes between two conditions using human population RNA-seq samples, we found a phenomenon by permutation analysis: two popular bioinformatics methods, DESeq2 and edgeR, have unexpectedly high false discovery rates. Expanding the analysis to limma-voom, NOISeq, dearseq, and Wilcoxon rank-sum test, we found that FDR control is often failed except for the Wilcoxon rank-sum test. Particularly, the actual FDRs of DESeq2 and edgeR sometimes exceed 20% when the target FDR is 5%. Based on these results, for population-level RNA-seq studies with large sample sizes, we recommend the Wilcoxon rank-sum test.

genomebiology.biomedcentral.com

Does anyone know the best and original references for absolute quantification of ChIP-Seq and RNA-Seq, using spike-in normalization?

Out today in @naturegenet.bsky.social -- PERFF-seq! With @tsionabay.bsky.social , @ronanchaligne.bsky.social, Bob Stickels, Meril Takizawa, + Ansu Satpathy, we describe this new assay to study rare populations with programmable nucleic acid cytometry. 1/n www.nature.com/articles/s41...

Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing - Nature Genetics

Programmable Enrichment via RNA FlowFISH by sequencing (PERFF-seq) isolates rare cells based on RNA marker transcripts for single-cell RNA sequencing profiling of complex tissues, with applicability t...

nature.com

Have a look at all the cute #nudibranchs pictures in our article just published in Microbiome! 🤩 We applied #museomics to a large collection of nudibranchs and discovered novel symbionts @i2sysbio.es @uv.es @csic.es #microsky #bioinformatics 👩‍🔬🦠🧪🧬🖥️🦑 🧵⬇️ link.springer.com/article/10.1...

Museomics reveals uncultured symbionts with biosynthetic potential in nudibranchs - Microbiome

Background Museum specimens are widely used for PCR-based pathogen detection, yet their potential for metagenomic discovery of beneficial microbes remains underexplored, largely due to difficulties in...

link.springer.com

Containers Rot Too: What happens when you try to rebuild containerized #bioinformatics tools from five years of software papers blog.stephenturner.us/p/containers... 🧬💻🧪. A new paper with friends and colleagues at @uvadatascience.bsky.social 1/

Containers Rot Too

What happens when you try to rebuild containerized bioinformatics tools from five years of software papers

blog.stephenturner.us

i see a particular grievance regularly on here: "a paper I reviewed came back to me at a diff journal. the authors didn't address my concerns at all." seriously what are you doing accepting to review the same paper? let people breathe & have another chance. let them decide what's worth addressing.

Matt Weiner@mattweiner19.bsky.social · 2w ago

will the next reviewer have the same objection? if you revise to address the objection, will the next reviewer say "I don't see why the paper spends so much time addressing this objection that no one could possibly have"? who knows

As also noted already over on mastodon where I saw your post first (as #rstats is laggy here...) -- this is all via a still-on-CRAN package by JJ cran.r-project.org/package=mani...

TIL protein language models exist — transformers trained on amino acid sequences that learn structure/function without explicit physics. Two great 2026 roundups comparing 18+ PLMs and 14 design tools: rewire.it/blog/protein... rewire.it/blog/protein...

Lightweight Text Analytics Workflows with DuckDB In this blog post, Petrica Leuca demonstrates how to use #DuckDB for keyword, full-text, and semantic similarity search with embeddings. Learn how to use DuckDB to efficiently perform advanced text analytics in Python: duckdb.org/2025/06/13/t...

This looks useful. A typical meta-analysis in ecology mixes experiments with observational studies, mixes coefficients with different controls and therefore different causal meanings. I would not normally say "hey the folks in medicine are doing it right, imitate them" but in this case maybe

Alfredo Sánchez-Tójar@asanchez-tojar.bsky.social · 3w ago

Are our ecological conclusions built on shaky foundations? Our latest paper in @methodsinecoevol.bsky.social highlights that Risk of Bias (RoB) assessment, crucial for ensuring the internal validity of research, is almost never used in #systematicreviews in eco & evo 📉 🔗 doi.org/10.1111/2041...

1. don't let the perfect be the enemy of the good; sometimes, refrain from seeking perfection when good will do fine. 2. Perfection is a moving target. Good is a finish line. Stop aiming for a masterpiece and start aiming for done. Progress only happens when you let "good enough" have its turn.

I have 30 jokes about the central limit theorem. That's normal, right?

Karandeep Singh@kdpsingh.bsky.social · 5mo ago

I have a joke about missing data, but

It's hard to do satire of a field that is continually self-satiring, but this is a valiant attempt: puregenius.education

The World's First Fully Automated Genius System

Experience the future of education with PureGenius - an AI-powered learning platform that unlocks every student's potential. Sign up for early access today.

puregenius.education

Every day is a good day for sharing one of the most useful papers about research data ever written. PLEASE get your people to understand and follow this advice. www.tandfonline.com/doi/full/10....

I think of the recommendations in this paper a bit like the Twelve Commandments of Spreadsheets... follow them and save yourself HOURS at the other end. We assume that students/researchers know this stuff, but no one has explicitly been taught it. Another hidden curriculum beauty...

Darren Dahly@statsepi.bsky.social · 5mo ago

Every day is a good day for sharing one of the most useful papers about research data ever written. PLEASE get your people to understand and follow this advice. www.tandfonline.com/doi/full/10....

I wanted to note that I made a list of all ancient comets from Med antiquity (500 BCE-400 CE) for class a number of years ago. Here is my excel sheet, based on Ramsay, Descriptive Catalogue of Greco-Roman Comets from 500 B.C. to A.D. 400. Syllecta Classica, 17. 2006. docs.google.com/spreadsheets...

Sarah E. Bond@sarahebond.bsky.social · 6mo ago

A set of researchers want Halley's Comet to be renamed 💫 "The monk Eilmer—or Aethelmaer—of Malmesbury must have been elderly when he saw Halley's Comet for the second time in 1066. He realized that he had also seen the same comet in 989." Not sure Eilmer really understood it cyclically but okay...

Discover SILVA 2026: Reliable 16S, 18S rRNA data from 2007! Global resource for microbial diversity, trusted by DSMZ, ELIXIR, & scientists. PMID:41251139, Nucleic Acids Res 2025, @NAR_Open https://doi.org/10.1093/nar/gkaf1247 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪

I feel so proud to have contributed in some way to this work (through ggplot2). It’s especially close to me because my mum has Alzheimer’s.

Eric Topol@erictopol.bsky.social · 7mo ago

The Shingles vaccine and reduction of dementia: a new natural experiment from Canada replicated 3 others and adds to this week's link to slowing of biological aging. erictopol.substack.com/p/spotlight-...

MaAsLin 3: refining and extending generalized multivariable linear models for meta-omic association discovery www.nature.com/articles/s41... #Rstats pkg github.com/biobakery/Ma...

They said it couldn't be done. They said it was impossible. They rejected my grant proposals. Now someone else has done it and it's published in Nature.

Breast milk isn't just nutrition – it delivers live bacterial strains that colonize the infant gut and persist for months. Happy to share our new paper, where we used metagenomics to track bacterial strains between 195 mother-infant pairs over the first 6 months of life: doi.org/10.1038/s414...

Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother’s milk - Nature Communications

Here, with metagenomic analyses on longitudinal samples collected from 195 mother-infant pairs, the authors show that the breast milk microbiome contributes to infant gut assembly through bacterial st...

doi.org

Yugioh card text is now at ~85 words per card for cards released in 2025, roughly a 200% increase since the games original release. #yugioh #anime #data #dataviz #rstats

This is a fantastic story I did not know. Ebright and his college roommate were once celebrated as the next Watson & Crick. Check out the acknowledgments in his first paper. Times sure have changed. www.pnas.org/doi/epdf/10....

Jeremy Berg@jeremymberg.bsky.social · last yr.

Seeing Richard Ebright's name reminds me of another recent thread... bsky.app/profile/jere... 1/n

Some interesting insights here, including that people are much more influenced by *people they follow* switching platforms than by their own *followers* switching platforms. Preprint: "Why Academics are Leaving Twitter for Bluesky" arxiv.org/abs/2505.24801

infoDOCKET@infodocket.bsky.social · last yr.

Preprint: "Why Academics are Leaving Twitter for #Bluesky" (via #arXiv) arxiv.org/abs/2505.24801 @bsky.app #socialmedia