SMT

Oh and the headline is 26-83x faster than minimap2 for transcriptome mapping (we're not doing spliced genomic mapping yet) with memory usage ~2.1G and similar accuracy (and equal or better quant so far). Feeling cute; may even eek out a little bit more before the preprint.

Announcing DuckDB 2.0.0 LTS “Cinnamon Teal” 🦆 This is the biggest #DuckDB feature release ever, and it's shipping a polished version of the Quack protocol for DuckDB-as-a-server, async I/O, a first-class VARIANT type, agent mode, triggers, an extensible SQL parser and more – read on for details.

We studied the evolution of genome-wide linkage disequilibrium and its influence on genetic architecture with genetic drift. We found that the Bulmer effect is population size and demography dependent. For nerds: genetic architecture follows from solving PDEs.

This is great, already bringing some conceptual clarity of something very generic. Let's see what one can do with libmizu in bioinformatics tasks like very high throughput pipelines under memory constrains

TokyoR enjoyed the world premiere of mizu today, and Mizu-chan stole the show: lock-free shared-memory parallelism for R, plus a Python binding on the same C core. Repos are open but pre-release, and the API will change. Feedback welcome on GitHub. github.com/shikokuchuo/... #RStats #Tidyverse

Update: corteza scored 100% on ARC-AGI-3's public set with GPT-6 Astra! And due to how they calculate their metrics, I'm happy to report that our 100% is the best 100%. I made a dashboard with details: cornball.ai/arc-agi-3/ #rstats

The truism that LLMs are LITERALLY stochastic parrots continues to butt-hurt some people. Why bother? You're literally operationalizing it through resampling, branching, verification, and search a.k.a. “agents”. Just show the promised value. Cure cancer. Long live Chinchilla!

#RStats heads-up CRAN Macos binaries are zstd compressed now (at least for some recently built ones, including knitr), this might break some CI setups github.com/r-lib/pkgdep...

New beta of #Rstats rig: LOTS of EXCITING stuff: - new: web site: rig.r-lib.org - new: user-mode R installation: rig.r-lib.org/admin-vs-use... - new: manage R packages (CRAN + git): rig.r-lib.org/pkg-guide.html - new: manage R projects and virtual environments: rig.r-lib.org/proj-guide.h...

CanardAbsurd: Durable #RStats workflows with DuckDB state and Quack remote SQL (Slop) Sloppy attempt to solve some recurring issues around durability (and resumption) especially for (frontend or api) exposed (costly) workflow coordination. repo: github.com/RGenomicsETL...

Long reads carry multiple small vars and SVs and their phasing. LongcallD is the only caller that tightly integrates germline/mosaic small/structural vars/MEIs and their phasing in a single C program. One command line to get competitive small variant calls and better SVs. Led by Yan Gao.

Big difference is obviously macros. But they worked damned hard to keep “the code is just data” philosophy that underpins macros.

Well, it's now backed by S3 and I've made the code public for anyone interested: github.com/vinimdocarmo... 🦆

The Futureverse Resource Specification proposal: a syntax for resource declarations, monitoring & scheduling; fits <- map(xs, model_fit) |> resources(\(x) memory(4*object.size(x))) |> futurize() www.jottr.org/2026/08/11/r... #RStats #parallel #hpc

Quack, quack! A DuckDB v2.0 preview is here! 🦆 In this post, #DuckDB co-creators Mark Raasveldt + @hannes.muehleisen.org preview the headline features of DuckDB v2.0 (expected to land this autumn): • DuckDB as a server • Triggers • async I/O • + more Dive into the deets: duckdb.org/2026/08/17/d...

Can databases scale scientific analyses beyond RAM? I’m excited to share dbverse, a composable database framework built to do just that. Across benchmarks, dbverse delivers ~1000x speedups and scales #spatialomics analyses to millions of cells. Preprint: www.biorxiv.org/content/10.6... 1/🧵

diffuseR is on CRAN! AI images and video, locally in #rstats install.packages("diffuseR") Go make something weird!

No matter how much one tries, LLMs cannot stop generating disgusting #Rstats code (1K .something functions checking if string is empty or similar) and i think this is getting worse. No wonder people do not want to read code anymore or prefer using slop language they don't know to read

CRISPR off-target search can find the right locus while hiding plausible alignments within it. I wrote about how Sassy v0.2.5 uses recursive backtracking to report every reasonable alignment—more than 9× as many in under 30 seconds. blog.fulcrumgenomics.com/p/why-crispr...

Even though i am a user of slopware, i thing the #Bioinformatics field needs a declaration like this leidendeclaration.ai

#CRAN Release of version 1.5.1-0.1.3 of Rduckhts: #RStats Bindings to the #htslib based #DuckDB extension for HTS file formats This comes with a BigWig reader via libBigWig used with (WIP)DuckVEP: the fastest Ensembl VEP-compatible consequence predictor in the West written in #C #Bioinformatics

#RStats is this SSL issue on cran.r-project.org/submit.html restricted to me or others are facing the same issue ?

#Rstats ah looks like CRAN fedora machine's tool chain got updated, and lot of C code nonsense in the vendored libraries my packages wrap are not allowed anymore. Good though that there are 25 other packages concerned :D I have on month to fix it or packages will be rightfully boot out

best way to send a LLM into a loop and burn all your tokens, in #RStats/C project, say go look at @coolbutuseless.bsky.social repos github.com/coolbutusele... for what we can use

CRAN release of version 1.4.0-0.1.0 of Rduckhts, the #RStats It was also nice to confirm that are our port of Brent Pedersen 's great mostdepth algorithm is likely the fastest for that application space in the West. But riker shows us there is space for memory bounding !

My secret 4th ALGO paper is out! We show a tight space lower on non-minimal k-perfect hash functions, generalize PtrHash into a non-minimal k-PHF, and then use it to develop a hash set implementation that is up to 1.6x faster than other hash sets! With Stefan {Hermann, Walzer} and Peter Sanders

ggmlR from Yuri Baramykov is a great #RStats package, i re-use the big work of the selective ggml build infra for the related Rfmalloc Project ggmlR: github.com/Zabis13/ggmlR Rfmalloc monorepo : github.com/sounkou-bioi...

This is for the real lovers of esoterica RSTT: Work-in-progress set-theoretic type algebra for the R language by Mickaël Laurent #RStats, #OCaml, #C API, Programming language theory and set theory repo : github.com/E-Sh4rk/rstt/ with a REPL !

My day job is to conduct statistical analysis of omics data, and most of it is spent writing R. In this new blog post, I share the R package shape I reached for in my recent projects. mickael.canouil.fr/posts/2026-0... #RStats #Shiny #Quarto #OpenSource #DataScience

since i am doing lot of pi based vibesloping these days and R markdown is my testing framework, made piknit #RStats package with Slope Code for a coming work github.com/sounkou-bioi...

cited Marx one time in a session, and now Slope Code autocompletes "idealist" at each new concepts "discovery". Below i suggest let's see what are the lazy eval/effect type of libraries in the Typescript (for my own culture) world just like in #RStats : --->Idealist

‼️Big package update on CRAN! #raymolecule v0.9.0 brings ribbon diagrams! Grab PDB files directly from the RCSB Protein Data Bank with just their PDB ID and render it in #RStats with #rayrender or #rayvertex: it's that easy! read_pdb("2w5o") |> generate_ribbon_scene() |> render_model()

Now you can use your Claude or ChatGPT subscription to run the R agent harness, corteza. No API key, no per-token meter, and it's on CRAN! Thanks to @hadley.nz for the provider-native search idea, and to @pp0196.bsky.social, whose Codex OAuth PR became tinyoauth. cornball.ai/posts/claude...

New release of secretbase 1.3.0 - a cryptography and data encoding toolkit. Adds base64 URL-safe variants. This is in addition to sha256, sha3, shake256, keccak, siphash, base58, cbor, json etc. all in 40kB. This package provides secure hashing for {targets}. #Rstats github.com/shikokuchuo/...

#Rstats package update: zip 3.0.0 with some very cool new things: password protected zip files, vectorized and concurrent unzip(), unzip over HTTP, progress bars. Full change log at github.com/r-lib/zip/re...

I’m excited to announce that #codex is now available (typically through a chatGPT subscription) from R through corteza. Logging in is enabled by the dev version of the new tinyoauth package, already in the CRAN queue! A big thank you to @pp0196.bsky.social for the contribution.

Beware #Rstats users, according to Misanthropic, an R to C transpiler is a security risk 😄 Fable turned out to as expected to be La Fable I think some french speaker at Misanthropic is doing some kind of joke with these model names

Rbebelm: #RStats Bindings for 'BebeLM' 'CPU' Inference For A 8B-1B Active model, not that bad A tiny R CLI "Agent" inspired by Corteza github.com/cornball-ai/... repo: github.com/sounkou-bioi... Upstream Rust crate : github.com/maximecb/beb... LFM2.5-8B-A1B blog: www.liquid.ai/blog/lfm2-5-...

RsimdDispatch: Runtime 'SIMD' Dispatch Templates for 'C' Code in #RStats Packages hellorust.multiversion: Minimal Rust SIMD Multiversioning Example for #RStats A way to enjoy both Linux binary Packages and Optimized code at runtime. github.com/sounkou-bioi... github.com/sounkou-bioi...

academic.oup.com/bioinformati...

Our medRxiv preprint is out: Automated versus manual reanalysis in rare disease genomics. We reanalysed 377 rare disease cases from a routine diagnostic genome sequencing cohort, comparing the established manual workflow with Talos-based automation. www.medrxiv.org/content/10.6...

We conducted the most extensive systematic GWAS gene prioritisation to date across all openly available data, with a retrospective analysis of 100,526 GWAS over the past decade: www.biorxiv.org/content/10.6...