AlphaGenome is out in @nature.com today along with model weights! 🧬 📄 Paper: www.nature.com/articles/s41... 💻 Weights: github.com/google-deepm... Getting here wasn’t a straight path. We discussed the story behind the model, paper & API in the following roundtable: youtu.be/V8lhUqKqzUc

AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates 🥨 www.biorxiv.org/content/10.6... 🧬💻🧪 github.com/marbl/anianns

I taught (and co-taught) a course on human population genetics from 2000-2024. Having retired, I'm now making all the course materials public: github.com/alanrogers/p... #popgen #evbio

Balancing selection alert!! 🧬🧪 New preprint where we try to quantify how likely (or rather, unlikely) it is for balancing selection to maintain stable polymorphism, and how easy (or rather, challenging) it is to identify its signatures in genomes. #Popgen #MolecularEvolution #EvoBio #Science

#Rstats {interprocess} : Mutexes, Semaphores, and Message Queues for R by Daniel P. Smith and co-workers github.com/cmmr/interpr...

I merged a PR for mirai today (fixing an esoteric bug), that came with a performance boost that I'd never have thought existed. That means that on my laptop, the default (with dispatcher) round-trip performance now dips into sub-100 microseconds territory!! Get it now: `pak::pak("r-lib/mirai")`

Automated #SQL formatting within #rstats files has just been added to the `duckdb-r-editor` #positron extension. github.com/belian-earth... ✌️

#dbt and #rstats friends, sorry about my past whining. I wrote up all my issues here to make your life easier, with even a tiny shoutout to #duckdb in there too! github.com/eriksquires/...

#Rstats #dplyr #ducdkb community extension by ChanYub Park Use dplyr synthax in #duckdb duckdb.org/community_ex...

#RStats is there a DuckLake package out there ? or should i stop raw-dogging sql strings and make a proper package for projects i am using DuckLake for

The #RStats ByteCode Book by @coolbutuseless.fosstodon.org.ap.brid.gy for lovers of esoterica coolbutuseless.github.io/book/rbyteco...

#RStats even when one (loosely) knows intellectually how it works, the event loop feels like magic Now, how would one make this (if possible at all) print "Got here i !"

orthogene: a Bioconductor package to easily map genes within and across hundreds of species www.biorxiv.org/content/10.6... #Rstats bioconductor.org/packages/ort...

Following an Rcpp question 'how do I share an object / external pointer' between #Rstats and #Python, I cooked up a simple 'stopwatch' example in two repos with two packages: github.com/eddelbuettel... github.com/eddelbuettel... The Python side is on PyPi, shall I send the R side to CRAN?

Maybe the fastest BCF/VCF to #RStats DataFrames using #htslib and #duckdb C API. Easily the title of fastest BCF/VCF to parquet convertors in #RStats (no other R options :D). This was motivated, among other things, by the idea of trying out #DuckLake in a familiar field github.com/RGenomicsETL...

Marxist analysis of the competing interests in the USian ruling class required here

acmgscaler: an R package and Colab for standardized gene-level variant effect score calibration within the ACMG/AMP framework academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/badonyi/acmg... #Rstats

Can MAVEs and population-free VEPs be combined to improve variant classification? VEPs detect a broad range of pathogenic variants, while MAVEs give more conservative & decisive calls. Combined, they equitably reclassify >90% of VUS. Read more in our study on combining evidence from MAVEs and VEPs:

#RStats #Paper Comparing R Bytecode Compilers Written in R, Java, and Rust (Extended Abstract) by Pierre Donat-Bouillud and Co-workers drops.dagstuhl.de/entities/doc... C version for segfault lovers: github.com/PRL-PRG/crbcc

The amount of slop from would-be technical managers coming our way when they get into CLI tools is going to be massive and will be one of the most important driver of Anti-LLM views in software adjacent fields

PSA: The long-lived "let us talk about anything and everything" related to #Rcpp mailing list 'rcpp-devel' at R-Forge seems to have moved on to another place where we cannot reach it. May its memory be a blessing. #rstats Going forward, let's try to connect at this link: github.com/RcppCore/Rcp...

I am increasingly using a macro to optimize allocations in #c #clang code either in stand alone C, or when writing #rstats and #perl extensions. The macro (the screeenshot for #perl is shown below) allocates on the stack unless one wants something big

I released {secretbase} 1.1.0 today. github.com/shikokuchuo/... Adds optimized base58check and CBOR encoding. This is a zero-dep #rstats package that wraps C code for hashing and binary/text encoding often needed in web development contexts. It also handles the file/object hashing for {targets}.

#RStats #duckdb #arrow gurus what is a "A scannable Arrow-object" and how one can implement suck a thing from nanoarrow streams if possible to avoid depending on the arrow package. Right now i convert some files into arrow IPC and use the duckdb nanoarrow extension on them for various purposes

you wondered by golang was based

#Rstats #GenomicsIO fraq: A high-throughput extensible toolkit for processing fastq data github.com/traversc/fraq

Alpine 3.23 #rstats binaries are now available at rpkgs.com. Subsequently, 3.21 entered EOL. Binaries will continue to be built until 3.24 has been released.

R2G2: A Python-R Framework for Seamless Integration of R/Bioconductor Tools into Galaxy www.biorxiv.org/content/10.6... #rstats 🧬🖥️🧪 github.com/BlankenbergL...

Our new preprint is out now! 🎉🎉🎉 Big news for everyone doing GWAS: We have updated LD score regression (LDSC) for the next generation of genomics.

#RStats bindings to Automerge CRDTs by Charlie Gao """enabling automatic merging of concurrent changes across distributed systems without conflicts. Work offline, collaborate in real-time, or sync across platforms—changes merge automatically."""" shikokuchuo.net/automerge-r/

Understanding the LLM-based gene embeddings www.biorxiv.org/content/10.6... 🧬🖥️🧪

Looks like this is not a macos crap but something about tinycc+R since I get the same bus error on a apparently "not signed" #RStats macos ci test. This is quite odd since a simple C test works and the bus error does not happen on Linux github.com/sounkou-bioi... github.com/sounkou-bioi...

As it happens that #RStats binary on macos runners seems to be hardened, the idea of C JIT from with tinycc on macos is mostly hopeless. Works fine on linux on the main and on macos in pure C. Looks like this is a know issue in other contexts blog.davisvaughan.com/posts/2022-0...

dtreg: Describing Data Analysis in Machine-Readable Format in Python and R arxiv.org/abs/2512.108... #Rstats

The fact that the state of the art #Bioinformatics solution for secondary analysis in #Genomics is closed source is sad pmc.ncbi.nlm.nih.gov/articles/PMC...

www.biorxiv.org/content/10.1... We finally submitted the earlier preprint to a journal after massive restructuring. We've expanded the REML section for those interested in the method. We clarify that ARG-LMM estimates mutational variance and not additive variance.

If eugenics is of concern, we need a coalition from a wide range of expertise together with engagements towards families seeking reproductive assistance. For instance, just complaining about the technical aspects of polygenic scoring is just too defensive, though looks *scientific*.

A youtube video for something i was actually looking for targets: Targets pipelines as R packages #targets #RStats www.youtube.com/watch?v=hxit...

@rohitsingh8080.bsky.social USHER: Guiding Foundation Model Representations through Distribution Shifts Aditya Pratapa, Purushothama Rao Tata, Rohit Singh bioRxiv 2025.11.20.689462; doi: doi.org/10.1101/2025...

Preprint Alert! With @tmthrz.bsky.social and @rayanchikhi.bsky.social we aim to tackle practical unitigs compression! A thread:

For my(misguided)project of #RStats CFFI gen along the lines of Rffi package, which in hindsight is becoming a poor C user's Rcpp reproduction, i came across this nice device for getting offsets and the horrible macros that go with it (but what can we do, this is C ) en.wikipedia.org/wiki/Offsetof

#Rstats gurus is there a way to declare a package linux only ? I know the OS_type unix specification but I need to restrict to linux. Because i use linux specific things and can't/don't want to put up with macos nonsense. Plus the packages are for genomics ETL I.e going to be on linux servers

New post on the @ropensci.org blog: How to Assess Usage of your #RStats Package 📂 Downloads 🌳 Reverse dependencies 🔍 Code mentions 🎓 Citations ⭐ Popularity measures: likes 🤝 Contributions to the repository 🙋 Use case reports 🕵️ Telemetry ropensci.org/blog/2025/12...

#Rstats treesitter.c: a 'data' package providing the #C grammar for use with the treesitter package. Since the CRAN submission, i ve added the fake libc headers from the Eli Bendersky's pycparser eli.thegreenplace.net/2015/on-pars... and some ridiculously slow R's installed headers parsing utils

One final contributing to base R post from me today, sharing a blog post from Rhian on her experience of participating in an R Dev Day. rhian.rbind.io/posts/2025-1... @statsrhian.bsky.social #RStats

I wrote a long thread about contributing to base R, highlighting the resources and opportunities provided by the R Contribution Working Group. contributor.r-project.org #RStats

#RStats wiith a little bit of codegen and libffi via RSimpleFFI, quick and dirty binding of the #Bioinformatics htslib library package : github.com/sounkou-bioi...

LorMe: a streamlined and interoperable R framework for end-to-end microbiome analysis www.biorxiv.org/content/10.1... #Rstats 🧬🖥️🧪 github.com/wangnq111/Lo...

Day 30 #30DayMapChallenge - Drone Strike Fatalities in Mali Did a makeover of the day 1 map but this time using {gganimate} and the entire dataset from ACLED. Worked out OK apart from the geom_sf_labels kept causing an error with the animation so I gave up on that. #rstats #dataviz

plinkQC: An Integrated Tool for Ancestry Inference, Sample Selection, and Quality Control in Population Genetics www.biorxiv.org/content/10.1... 🧬🖥️🧪 R package meyer-lab-cshl.github.io/plinkQC/ #Rstats