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SMT

@pp0196.bsky.social

#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

$Rduckhts: 'DuckDB' 'HTS' File Reader Extension for 'R' Bundles the 'duckhts' 'DuckDB' extension for reading 'HTS' file formats (VCF/BCF, SAM/BAM/CRAM, FASTA, FASTQ, GFF, GTF, tabix) from 'R' via 'DuckDB'. The extension and its 'htslib' dependency are compiled from vendored sources during package installation. Authors:Sounkou Mahamane Toure [aut, cre], htslib authors [ctb], DuckDB C Extension API authors [ctb] Rduckhts_0.1.1-0.0.1.tar.gz Rduckhts_0.1.1-0.0.1.zip(r-4.6)Rduckhts_0.1.1-0.0.1.zip(r-4.5)Rduckhts_0.1.1-0.0.1.zip(r-4.4) Rduckhts_0.1.1-0.0.1.tgz(r-4.6-any)Rduckhts_0.1.1-0.0.1.tgz(r-4.5-any) Rduckhts_0.1.1-0.0.1.tar.gz(r-4.6-any)Rduckhts_0.1.1-0.0.1.tar.gz(r-4.5-any) Rduckhts.pdf |Rduckhts.html✨ Rduckhts/json (API) NEWS # Install 'Rduckhts' in R: install.packages('Rduckhts', repos = c('https://rgenomicsetl.r-universe.dev', 'https://cloud.r-project.org')) Bug tracker:https://github.com/rgenomicsetl/duckhts/issues0 issues On CRAN: no 3.75 score 12 exports 2 dependencies Last updated0 hours ago from:e99a28a305. Checks:7 OK, 1 NOTE, 1 FAIL. Indexed: yes. Citation To cite package ‘Rduckhts’ in publications use: Toure S (2026). Rduckhts: 'DuckDB' 'HTS' File Reader Extension for 'R'. R package version 0.1.1-0.0.1, https://github.com/rgenomicsetl/duckhts. Corresponding BibTeX entry: @Manual{, title = {Rduckhts: 'DuckDB' 'HTS' File Reader Extension for 'R'}, author = {Sounkou Mahamane Toure}, year = {2026}, note = {R package version 0.1.1-0.0.1}, url = {https://github.com/rgenomicsetl/duckhts}, }$ $Rduckhts: DuckDB HTS File Reader Extension for R Rduckhts provides an R interface to a DuckDB HTS (High Throughput Sequencing) file reader extension. This enables reading common bioinformatics file formats such as VCF/BCF, SAM/BAM/CRAM, FASTA, FASTQ, GFF, GTF, and tabix-indexed files directly from R using SQL queries via duckhts. How it works Following RBCFTools, tables are created and returned instead of data frames. VCF/BCF, SAM/BAM/CRAM, FASTA, FASTQ, GFF, GTF, and tabix formats can be queried. We support region queries for indexed files, and we target Linux, macOS, and RTools. htslib 1.23 is bundled so build dependencies stay minimal. The extensnion is built by adapting the generic extension infracstructure by using only makefiles unlike unlike the submitted communtity extension duckhts. Installation The package can be installed from github remotes::install_github( "RGenomicsETL/duckhts", subdir = "r/Rduckhts")`. System Requirements Installation requires htslib dependencies such ad zlib and libbz2, and optionally for full functionally liblzma, libcurl, and openssl. The package requires GNU make. On Windows’s Rtools, htslib plugins are not enable.$

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

February 9, 2026 at 9:00 PM

SMT

@pp0196.bsky.social

This is big !

February 9, 2026 at 8:53 PM

Reposted by SMT

Charlie Gao

@shikokuchuo.net

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/

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.

tidyverse.org

February 9, 2026 at 8:13 PM

Reposted by SMT

Christos Argyropoulos MD PhD

@christosargyrop.mastodon.social.ap.brid.gy

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.

February 8, 2026 at 6:28 AM

Reposted by SMT

troy_phd

@troyhernandez.bsky.social

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...

The Tinyverse Development Toolchain

Every R package we’ve released over the past two weeks was built with the same set of tools. Today we’re making those tools public. The sidequest eraCLI coding tools like Claude Code (and even llamaR!...

cornball.ai

February 6, 2026 at 4:27 PM

Reposted by SMT

Brenden

@beesm.bsky.social

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...

GitHub - brendensm/sqlfluffr: R Wrapper to the SQL Linter and Formatter 'sqlfluff'

R Wrapper to the SQL Linter and Formatter 'sqlfluff' - brendensm/sqlfluffr

github.com

February 6, 2026 at 9:13 PM

SMT

@pp0196.bsky.social

#RStats Rtinycc : Builds 'TinyCC' 'Cli' and Library for 'C' Scripting in 'R'

Package Link for Segfault lovers: github.com/sounkou-bioi...

Rtinycc is an R interface to TinyCC, providing both CLI access and a libtcc-backed in-memory compiler. It includes an experimental FFI inspired by Bun’s FFI for binding C symbols with predictable type conversions and pointer utilities. The package targets Unix-alike systems and focuses on embedding TinyCC and enabling JIT-compiled bindings directly from R. Combined with treesitter.c, which provides C header parsers, it can be used to rapidly generate declarative bindings.

February 7, 2026 at 7:05 PM

Reposted by SMT

Žiga Avsec

@avsecz.bsky.social

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

January 28, 2026 at 9:02 PM

Reposted by SMT

Stephen Turner

@stephenturner.us

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

January 29, 2026 at 3:00 PM

Reposted by SMT

Alan Rogers

@alanrogers.bsky.social

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

GitHub - alanrogers/popgen: A course on population genetics

A course on population genetics. Contribute to alanrogers/popgen development by creating an account on GitHub.

github.com

November 27, 2025 at 7:10 PM

Reposted by SMT

Aida Andres

@aidaandres.bsky.social

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

Max Reuter @maxreuter.bsky.social · 20d

A new preprint from the lab, with postdoc @deboraycb.bsky.social and collaborators @aidaandres.bsky.social and Tim Connallon:

“Characterising the detectable and invisible fractions of genomic loci under balancing selection”
www.biorxiv.org/content/10.6...

www.biorxiv.org

January 21, 2026 at 4:11 PM

SMT

@pp0196.bsky.social

#Rstats

{interprocess} : Mutexes, Semaphores, and Message Queues for R by Daniel P. Smith and co-workers

github.com/cmmr/interpr...

GitHub - cmmr/interprocess: Mutexes, Semaphores, and Message Queues for R

Mutexes, Semaphores, and Message Queues for R. Contribute to cmmr/interprocess development by creating an account on GitHub.

github.com

January 27, 2026 at 10:58 PM

Reposted by SMT

Charlie Gao

@shikokuchuo.net

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")`

January 26, 2026 at 9:04 PM

SMT

@pp0196.bsky.social

github repo with the code github.com/sounkou-bioi...

GitHub - sounkou-bioinfo/mirai.plumber2.duckdb: "Minimal" `duckDB` + `mirai` + `plumber2` example

"Minimal" `duckDB` + `mirai` + `plumber2` example. Contribute to sounkou-bioinfo/mirai.plumber2.duckdb development by creating an account on GitHub.

github.com

January 27, 2026 at 9:05 PM

SMT

@pp0196.bsky.social

added has comment to your gist

January 27, 2026 at 8:43 PM

SMT

@pp0196.bsky.social

if i get time, i will put a strip down gist marginally less invoved compared to @jrosell.bsky.social's one here gist.github.com/jrosell/e482...
But the setup is your own personal databricks if you had a good computation partitionner :D

Example of an async JSON API in R using dbplyr, SQLite, S7, plumber2 and mirai.

Example of an async JSON API in R using dbplyr, SQLite, S7, plumber2 and mirai. - async-json-api-plumber2-mirai-S7-DBI.R

gist.github.com

January 27, 2026 at 2:15 PM

SMT

@pp0196.bsky.social

You setup mirai deamons that will process the queries
run mirai::everywhere to setup connections and other bookkeeping (example caching ) and run

I used similar strategy to what is explained below where my endpoints needed read only duckdb connections and cache_httpfs

github.com/posit-dev/pl...

async = TRUE · Issue #48 · posit-dev/plumber2

I want to use the programable API with mirai and the docs/website is not very clear. Is async=TRUE deprecated?

github.com

January 27, 2026 at 2:13 PM

Reposted by SMT

hughagraham.bsky.social

@hughagraham.bsky.social

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

January 27, 2026 at 1:06 AM

Reposted by SMT

Totoro

@nigelsq.bsky.social

#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/...

GitHub - eriksquires/dbt_wrong: Everything I did wrong with DBT

Everything I did wrong with DBT. Contribute to eriksquires/dbt_wrong development by creating an account on GitHub.

github.com

January 25, 2026 at 6:42 PM

SMT

@pp0196.bsky.social

#Rstats #dplyr #ducdkb community extension by ChanYub Park

Use dplyr synthax in #duckdb
duckdb.org/community_ex...

January 26, 2026 at 8:16 PM

SMT

@pp0196.bsky.social

#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

January 26, 2026 at 8:03 PM