really don t like that in order to read/write arbitrary nested parquet types in #RStats (as of now and to the best of my knowledge) you need to have the huge ( in the sense of compile time) duckdb or arrow dependencies. With the very good {nanoparquet}, you can avoid reader errors...

open.spotify.com/track/2W2S5e... #amapiano

If you were thinking about #ducklake in #rstats here is a blogpost that can help you get started.

R that travels light on #Linux: Portable R AppImages. Now working everywhere: your Ubuntu, friend's Fedora, cousin's Arch setup (btw) No sudo, no tears, just base R science ✨ (package support coming soon!) #RStats #AppImage #DataScience

Augmenting cost-effectiveness in clinical diagnosis using extended whole-exome sequencing: SNVs, SVs, and beyond. #WES #SNVs #SVs #Genomics #Bioinformatics #JournalOfHumanGenetics 🧬 🖥️ www.nature.com/articles/s10...

Benchmarking large language models for genomic knowledge with GeneTuring. #LLMs #Genomics #Bioinformatics @biorxivpreprint.bsky.social 🧬 🖥️ www.biorxiv.org/content/10.1...

Um, nobody tell @ocks.org, but I got #RStats WebR working in @observablehq.com Desktop… #DontTryThisAtHome #UnsafeComputing

Our latest blog post is about Kubernetes! Our very own Shane Halloran shares real-world lessons from deploying Posit Workbench on Azure Kubernetes Service (AKS), including practical debugging tips, and the importance of looking beyond the cluster when issues arise. #RStats #Kubernetes #Azure

Linux support 🐧 Same #rshiny → desktop workflow on #Fedora 42 aarch64: shinyelectron::export() → #rshinylive → #AppImage → portable #Linux app Plot twist: no more "go buy yourself a real computer" moments - you get zero #rstats dependencies too! The condescending Unix users have won this round.

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N

We evaluate two possible explanations for this increase: a) cfDNA increases due to excess cell death b) cfDNA increases because it cannot be cleared efficiently Our data consistently suggests an impairment in cfDNA clearance in the liver, challenging previous literature. (2/3)

MetaGLIMPSE: Meta Imputation of Low Coverage Sequencing Data for Modern and Ancient Genomes www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/karinkumar/M...

Hi everyone! Check my journal club talk on the latest review paper: Cell-type deconvolution methods for spatial transcriptomics 🧬 🎥 www.youtube.com/watch?v=xDjF... 🛝 speakerdeck.com/manishabarse @lieberinstitute.bsky.social #Bioinformatics #SpatialTranscriptomics #Cell-TypeDeconvolution

#RStats #C #assembly gurus Would be great to get rdyncall back on CRAN github.com/hongyuanjia/... i.e allowing R to be a lowkey systems programming language without the usual C API boilerplate

@coolbutuseless.fosstodon.org.ap.brid.gy's #rstats C API articles for the {callme} package are very good coolbutuseless.github.io/package/call...

Value semantics at scale with #Cpp github.com/arximboldi/i... #rustlang equivalent github.com/orium/rpds should not be too difficult to make #RStats bindings of any of the two #immutability #headerOnly #Cpp14

There is a secret joy in segfaults in #C when one spends most of their time in higher level languages, the direct OS/hardware interaction 😂

tok is back on CRAN! tok is @hf.co tokenizers for #rstats. It uses the same Rust libray as the python interface. It's pretty fast and fully compatible with tokenizers.json available on hub. See the release notes: github.com/mlverse/tok/...

tiny ( <400loc) implementation of Gemma3 270M using torch for #rstats github.com/mlverse/minh... Includes support for loading weights from hugging face hub.

The third agent in my AI-assisted rare disease workflow, the Variant Agent, is complex enough to need two posts! This first post describes the processing needed to get genomic variants annotated and inserted into a database. #OpenAI #Genomics #Bioinformatics jeffjjohnston.github.io/2025/08/24/v...

#OldieButGoodies #RStats #FunctionalProgramming Lazy List Implementations by Luke Tierney noweb : homepage.divms.uiowa.edu/~luke/R/lazy... Rscript : homepage.divms.uiowa.edu/~luke/R/lazy...

Fast and generic vectors in C by attractive chaos #include "kvec.h" Ref : attractivechaos.wordpress.com/2008/09/22/a... #C #MacroMagic #Generics

#GWAS #PopulationGenomics #BIAS #PRS academic.oup.com/gigascience/...

Just want to share this wild revision history of the Wikipedia page on Linkage Disequilibrium where Felsenstein himself debated people on the correct use of notations & definitions. After 100 years of #popgen people does not seem to be totally agree on what LD is? en.wikipedia.org/wiki/Talk:Li...

The GenomicRanges (github.com/BiocPy/GenomicRanges) package for Python got a major speed boost (v0.7.0+) thanks to Aaron’s blazing-fast C++ nclist interval indexing! #Bioinformatics #Genomics #Bioconductor

Facebook's #CPython runtime github.com/facebookincu...

HiRSE Summer of Programming Languages explored what different languages are good for. I talked about #rstats: https://youtu.be/92Sixju0qYQ&list=PLzCxBiTw83ujLTspm2lP6fMMHQkJaz7kc Other talks: #python https://youtu.be/nGpRvzGyM20&list=PLzCxBiTw83ujLTspm2lP6fMMHQkJaz7kc #fortran […]

Somebody had to try it: linear algebra on an OLAP and an OLTP database in R factbased.blogspot.com/2023/02/larg... Much older approach with even a proposed patch to GNUR (not required anymore with ALTREP) RIOT: I/O-Efficient Numerical Computing without SQL arxiv.org/abs/0909.1766 #rstats

#rstats Dev Diary WIP: Using {leopard} to capture device output, then manually render in {minipdf}

This Macros magic strategy may be useful on top of usual #RStats C API Macros for user functions [ great to have exact matching between R and .Call arguments with even the default values] #C #Programming #RStats ref : x.com/vkrajacic/st...

A proposal for an iterator protocol for the #Rstats `for` special primitive by Tomasz Kalinowski R-devel thread : stat.ethz.ch/pipermail/r-... Pull request : github.com/r-devel/r-sv... Very interesting discussion thread, hope it gets merged

In case it's not clear (yeah okay probably not), this changes the way search UI works in VSCode. It feels great with keyboard driven workflows via the command palette etc. You get search results in a editor window, with context around them. You can use 'jump to definition' or ctrl + click on them.

Help needed 🙏 If you're a HPC #RStats user on SGE/Slurm/Torque/PBS/LSF/OpenLava, could you pls try {future.batchtools} devel version per future.batchtools.futureverse.org/index.html#p...? library(future.batchtools) plan(batchtools_slurm) f <- future(Sys.info()) value(f) #parallel #hpc #future

#rstats #statistics I've released my new open source book, "Powered by Linear Algebra: the role of matrices and vector space in data science," at matloff.github.io/WackyLinearA.... Turns the classic LA course on its head! Still proves the theorems, but with a deep emphasis on applications.

timing may not be great given the recent re-organization at github, but browsing #Bioconductor source code and packages is going to be nicer (for now at least) when the package sources and the build system are transitioned to github - #r-universe github.com/bioconductor... #rstats #Bioinformatics

Situation among the military in Bamako right now is very serious, yet very opaque, too. Fair to say it's a make or break situation for the regime

As Urbanek reminded here, S was about providing an interactive environment for running fortran routines ! With R it got more Lisp like www.youtube.com/live/8je9tZB...

@schochastics.net has a great blog post about {base} R. blog.schochastics.net/posts/2024-0...

Taking inspiration from the ridiculous microbenchmark, made a LLM generate functions for generating actual nested loops functions after feeding it the #RStats language definition,Luke Cherney's codetools and some gratuitous #tailcall for the connaisseurs sounkou-bioinfo.github.io/ridiculousBu...

#kmers #Bioinformatics #Ancestry #lowpass Dependencies: #RStats #Perl #samtools #GenomeTester4

#Rstats thank you Luke Tierney/R Core 😂 Doing as good as the snake in interpreted loops despite massive corporate investment on that other side and the fundamental issues with R's homoiconic nature Note: CPython 3.14 might be faster, they are getting a jit thanks to Microsoft

#RStats #duckdb gurus, is thread safety the main reason we don't have (as of today) R level user defined functions like the duckdb's snake binding ? Or the reason is that we don't really have scalar functions ? github.com/duckdb/duckd...

#Rstats #Bioinformatics

#rstats Dev Diary - PDF creation in pure R I just figured out how to correctly construct RGB pixels with a separate Alpha channel.

#rstats #async #minimalism #oldiebutgoodie github.com/s-u/background

Looking at the command line, it seems to be using #Perl along with the Perl Data Language (PDL) (look at the ndarray in the screenshot). PDL is an extremely performant (much more than any #python alternative) autothreading library Shameless plug for my pages 👇 chrisarg.github.io/Killing-It-w...

There are a couple. metacpan.org/pod/Statisti... is the one I used with #Rstats v3 (I actually have not tested it with v4) and I was a user of RSPerl eons ago.

🧵 of takeaways messages and quotes....

Dan Sugalski has an interesting explanation about the #perl LOC weatherishappening.network/@wordshaper/...

@phoenixtrap.com @pp0196.bsky.social In metacpan.org/pod/Bio::Seq... the opt handler for #Perl was generated from the one I wrote for the #Rstats cmdline by #GPT4 In arxiv.org/abs/2406.10271 the #Rstats code was prompted based on Perl (stashes in Perl & environments in R are similar concepts)