SMT

#rstats 4.5.3 "Reassured Reassurer" scheduled for March 11. Full schedule on developer.r-project.org (or the svn if you're impatient.) This should be the wrap-up release for the 4.5 series.

Foto of a feminine nonbinary person in a purple floral shirt in front of a purple poster. The poster is displaying a structural equation model analysing the influence of parental education on children’s school grades. The person is smiling cheekily to the side.

Foto of a child with four fluffy buns and blue sunglasses. The child has lowered the sunglasses below their nose and is gazing over them.

Hi, I’m this week’s curator, Josi! I‘m a PhD student in statistical genetics 🧬 and use #RStats to do #SEM. I dabble in #DataViz and recently wrote my first #Rpackage. My hobbies are reading #Fantasy books 📚 and #maximalism. You may catch me at a conference matching my outfit to my poster 🤓🧜🏽‍♀️ #rladies

#RStats #tinyverse gurus: is their a mutation testing package out there that is compatible with {tinytest} ?

tinyverse vs ....

SMT (@bioinfhotep@genomic.social) Attached: 4 images #Genomics #Bioinformatics Release of duckhts: #htslib based #Duckdb Extension for High Throughput Sequencing File Formats https://duckdb.org/community_extensions/extensions/duckh...

#Duckdb #htslib #Genomics #Bioinformatics #RStats

duckths: Read HTS (VCF/BCF/BAM/CRAM/FASTA/FASTQ/GTF/GFF) files in DuckDB via htslib

Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension
genomic.social/@bioinfhotep...

base R packages

dtplyr: Data Table Back-End for 'dplyr' Provides a data.table backend for 'dplyr'. The goal of 'dtplyr' is to allow you to write 'dplyr' code that is automatically translated to the equivalent, but usually much faster, data.table code.

i guess you can always use this package cran.r-project.org/web/packages...

link is broken

GitHub - r-tooling/r4r: Monorepo for everything linked to the r4r project Monorepo for everything linked to the r4r project. Contribute to r-tooling/r4r development by creating an account on GitHub.

R4R is a tool for creating a reproducible environment from a dynamic program trace, from our lab in Prague.

From a R script/notebook, it generates a Docker image that contains everything to run the R code and reproduce the results.

Try it out!

Also with an article at ACM REP 2025

GitHub - PRL-PRG/rcp Contribute to PRL-PRG/rcp development by creating an account on GitHub.

#RStats Interesting Work to follow from Workers in the Vitek group

crbcc: R bytecode compiler implemented in C

github.com/PRL-PRG/crbcc

rcp : Copy-and-Patch JIT Compiler for R

github.com/PRL-PRG/rcp

Nallo: a Nextflow pipeline for comprehensive human long-read genome analysis AbstractMotivation. Long-read sequencing (LRS) is increasingly used for human medical research and clinical diagnostics, due to its capacity to generate co

Say hello to Nallo - our Nextflow pipeline for long-read WGS analysis!👋 It handles both ONT and PacBio data and we’re using this for rare disease and population projects in Sweden. A big team effort by Felix Lenner, Anders Jemt et al.🧬💻 academic.oup.com/bioinformati...

#RStats When i was looking at some of the perf in quickr readme, i was thinking oh these tails are R's garbage collection pauses, the R-to-C (LLM enabled) rabbit hole i went in makes the pauses worse because it is really R to R's C API and sometimes calling into R via Rf_eval :D

I love R for everything statistics, but I've always been a little jealous of statisticians using SPSS Complex Samples or SAS SURVEYSELECT to design their samples.

So I decided to build samplyr, a tidy and pipe-friendly grammar for survey sampling design in #rstats.

dickoa.gitlab.io/samplyr/inde...

Feb. update to the LLM+R guide 💪

8 new packages including:
code review, predictive modeling, speech-to-text, text-to-speech, HuggingFace integration, Gemini CLI companion, a CLI coding agent written in R🤯 ,and more!

available in English 🇱🇷 and Spanish 🇲🇽
luisdva.github.io/llmsr-book/
#rstats

#tinycc based #RStats #C #Transpiler, only 4x slower than #{quickr} for the convolution benchmark ! 2-3x faster than naive #C + marshaling. #tinycc transpilation will have an obvious advantage since it can always fallback when transpiling and use `Rf_lang3` since it has access to R's C runtime !

GitHub - r-xla/tengen Contribute to r-xla/tengen development by creating an account on GitHub.

#Rstats #HPC gurus
Is there a package for mixed precision arithmetic that covers most of the exotic new floating points or one needs specialized ML package from the r-xla organization like tengen github.com/r-xla/tengen

GitHub - eddelbuettel/r2u: CRAN as Ubuntu Binaries CRAN as Ubuntu Binaries. Contribute to eddelbuettel/r2u development by creating an account on GitHub.

First thing to do when you open a #Rstats project in #codex webapp, copy paste the r2u installation docs github.com/eddelbuettel... and tell it to write #Rstats scripts for R package dev instead of snake crap (they RL perl out this model for some unknown reason)

#RStats #Statsky
Any references and packages out there on statistical inference around binary outcomes for whom some outcome have no measurement error but the other has ? Should i just use linear models and get over it ?

GitHub - comp-med/r-ofhelper: Utility R package for the Our Future Health DNAnexus Trusted Research Environment Utility R package for the Our Future Health DNAnexus Trusted Research Environment - comp-med/r-ofhelper

For those of us R-users who are working with/on #dnanexus (specifically the Our Future Health TRE), I've written a small #rstats package to interact with their `dx` utility and submit jobs (among other things): github.com/comp-med/r-o...

#Rstats to avoid if/else and switch death in this project, a functional and centralized (reviewable) definition of the rules for future improvements, i thought that #{lambda.r} package's (by Brian Lee Yung Rowe) pattern matching would be great

github.com/zatonovo/lam...

#RStats the comparison results with #{quickr} is expected since tinycc is not an optimizing compiler like gfortran/flang, but still since you don t need an additional compiler at runtime and you can iterate (more segfault :D) very fast ! (no windows support for now/never)

this is great, better use this than configure/configure.ac !

GitHub - devOpifex/builder: Preprocessor for R Preprocessor for R. Contribute to devOpifex/builder development by creating an account on GitHub.

Happy to release builder: a preprocessor for #rstats.

You get a build step with macros, conditionals, directives, preflight, etc. along with new language features like fstrings, a deconstructor, and more.

github.com/devOpifex/bu...

Rduckhts: 'DuckDB' 'HTS' File Reader Extension for 'R' Bundles the 'duckhts' 'DuckDB' extension for reading 'HTS' file formats (VCF/BCF, SAM/BAM/CRAM, FASTA, FASTQ, GFF, GTF, tabix) from 'R' via 'DuckDB'. The extension and its 'htslib' dependency are compiled from vendored sources during package installation. Authors:Sounkou Mahamane Toure [aut, cre], htslib authors [ctb], DuckDB C Extension API authors [ctb] Rduckhts_0.1.1-0.0.1.tar.gz Rduckhts_0.1.1-0.0.1.zip(r-4.6)Rduckhts_0.1.1-0.0.1.zip(r-4.5)Rduckhts_0.1.1-0.0.1.zip(r-4.4) Rduckhts_0.1.1-0.0.1.tgz(r-4.6-any)Rduckhts_0.1.1-0.0.1.tgz(r-4.5-any) Rduckhts_0.1.1-0.0.1.tar.gz(r-4.6-any)Rduckhts_0.1.1-0.0.1.tar.gz(r-4.5-any) Rduckhts.pdf |Rduckhts.html✨ Rduckhts/json (API) NEWS # Install 'Rduckhts' in R: install.packages('Rduckhts', repos = c('https://rgenomicsetl.r-universe.dev', 'https://cloud.r-project.org')) Bug tracker:https://github.com/rgenomicsetl/duckhts/issues0 issues On CRAN: no 3.75 score 12 exports 2 dependencies Last updated0 hours ago from:e99a28a305. Checks:7 OK, 1 NOTE, 1 FAIL. Indexed: yes. Citation To cite package ‘Rduckhts’ in publications use: Toure S (2026). Rduckhts: 'DuckDB' 'HTS' File Reader Extension for 'R'. R package version 0.1.1-0.0.1, https://github.com/rgenomicsetl/duckhts. Corresponding BibTeX entry: @Manual{, title = {Rduckhts: 'DuckDB' 'HTS' File Reader Extension for 'R'}, author = {Sounkou Mahamane Toure}, year = {2026}, note = {R package version 0.1.1-0.0.1}, url = {https://github.com/rgenomicsetl/duckhts}, }

Rduckhts: DuckDB HTS File Reader Extension for R Rduckhts provides an R interface to a DuckDB HTS (High Throughput Sequencing) file reader extension. This enables reading common bioinformatics file formats such as VCF/BCF, SAM/BAM/CRAM, FASTA, FASTQ, GFF, GTF, and tabix-indexed files directly from R using SQL queries via duckhts. How it works Following RBCFTools, tables are created and returned instead of data frames. VCF/BCF, SAM/BAM/CRAM, FASTA, FASTQ, GFF, GTF, and tabix formats can be queried. We support region queries for indexed files, and we target Linux, macOS, and RTools. htslib 1.23 is bundled so build dependencies stay minimal. The extensnion is built by adapting the generic extension infracstructure by using only makefiles unlike unlike the submitted communtity extension duckhts. Installation The package can be installed from github remotes::install_github( "RGenomicsETL/duckhts", subdir = "r/Rduckhts")`. System Requirements Installation requires htslib dependencies such ad zlib and libbz2, and optionally for full functionally liblzma, libcurl, and openssl. The package requires GNU make. On Windows’s Rtools, htslib plugins are not enable.

Quick Start The extension is loaded with rduckhts_load(con, extension_path = NULL). We can create tables with rduckhts_bcf, rduckhts_bam, rduckhts_fasta, rduckhts_fastq, rduckhts_gff, rduckhts_gtf, and rduckhts_tabix using the parameters documented in their help pages library(DBI) library(duckdb) library(Rduckhts) ext_path <- system.file("extdata", "duckhts.duckdb_extension", package = "Rduckhts") fasta_path <- system.file("extdata", "ce.fa", package = "Rduckhts") fastq_r1 <- system.file("extdata", "r1.fq", package = "Rduckhts") fastq_r2 <- system.file("extdata", "r2.fq", package = "Rduckhts") con <- dbConnect(duckdb::duckdb(config = list(allow_unsigned_extensions = "true"))) rduckhts_load(con, extension_path = ext_path) #> [1] TRUE rduckhts_fasta(con, "sequences", fasta_path, overwrite = TRUE) rduckhts_fastq(con, "reads", fastq_r1, mate_path = fastq_r2, overwrite = TRUE) dbGetQuery(con, "SELECT COUNT(*) AS n FROM sequences") #> n #> 1 7 dbGetQuery(con, "SELECT COUNT(*) AS n FROM reads") #> n #> 1 10

FASTA, BAM, FASTQ, READER

#RStats
Rduckhts: 'DuckDB' 'HTS' File Reader Extension for 'R'

Sitting on the shoulders of the great #htslib API and the duckdb C API

Package : rgenomicsetl.r-universe.dev/Rduckhts

This is big !

nanonext 1.8.0 nanonext 1.8.0 adds a low-level streaming HTTP/WebSocket server to R's web infrastructure, with TLS support, new async primitives, and redesigned documentation.

nanonext 1.8.0 is out - R now has a streaming HTTP/WebSocket server with bundled TLS.

Runs alongside Shiny in the same process. We're already using it at Posit to explore new real-time capabilities.

#Rstats #tidyverse

tidyverse.org/blog/2026/02/nanonext-1-8-0/

I decided to write a paper (a technical note in #rstats) using one of the frontier models available through github copilot.
Everything will be documented ofc, but the draft of the intro is not promising: numerous subtle mistakes that are easily missed if you don't know the topic.

For our recent package releases, I’ve been using a lightweight, AI-friendly R workflow built around `littler` and 4 new tinyverse-inspired development packages we released today!
#rstats #tinyverse #ClaudeCode
cornball.ai/posts/tinyve...

Any #rstats folks interested in testing out a package for SQL linting in R workflows?

I made a package that wraps SQLFluff into R with reticulate. I've tried it on a few machines I own but would appreciate some experimentation before I try to send it to CRAN.

github.com/brendensm/sq...