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hughagraham.bsky.social
@hughagraham.bsky.social
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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 FASTA, BAM, FASTQ, READER
February 9, 2026 at 9:00 PM
Reposted
jakubnowosad.com
Honored and excited to be part of useR! 2026

I will give a keynote on geocomputation and spatial data science in R.

📅 6–9 Jul 2026, Warsaw, Poland
🔗 user2026.r-project.org

Let’s make this event spatial!

#useR2026 #RStats #RSpatial #Geocompr
Conference logo
February 8, 2026 at 4:02 PM
Reposted
mdcatchen.bsky.social
nolanlawson.com/2026/02/07/w...
We mourn our craft
I didn’t ask for this and neither did you. I didn’t ask for a robot to consume every blog post and piece of code I ever wrote and parrot it back so that some hack could make money off o…
nolanlawson.com
February 7, 2026 at 11:29 PM
Reposted
milesmcbain.bsky.social
Bit of love for #rstats 📦 {paint} today as I had to swap out a deprecated dependency.

The interactive scrolling ipaint() got a speed up, and some additional controls to advance pages, or to start / end. I find myself using this one a bit lately.
February 8, 2026 at 6:39 AM
Reposted
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
Reposted
tess-lab.org
Want to make your research more transparent, reusable, and impactful? I’ve written a practical Open Research primer with clear guidance, especially for geospatial ecology & geography — but useful across disciplines.
tess-lab.org/resources/op...

I'm passionate about open research throughout my work
February 5, 2026 at 10:24 PM
Reposted
kurtschwehr.bsky.social
TIL more than just gdal_translate can use all the CPU cores for decompression. So, pass `--config GDAL_NUM_THREADS=ALL_CPUS` to gdalinfo for massive compressed files! 🚀

github.com/OSGeo/gdal/i...
crschmidt: When running gdalinfo -stats on a large GeoTIFF, it uses only one core to compute stats. It would be nice if (for thread-safe datasets) it could run with more than one core. (Seems like this might be more practical now that https://gdal.org/en/stable/development/rfc/rfc101_raster_dataset_threadsafety.html is in place?) In particular, running gdalinfo -stats on CAFA_2020 from https://drive.google.com/corp/drive/folders/1exF1KpGr0EJqZ10yqPIkzqLfh6gGj3Sa took 8 minutes on my Macbook with an M3 chip, which seems like it could have gone faster with multi-threading. <snip> rouault @crschmidt Wouldn't https://gdal.org/en/latest/programs/gdal_dataset_check.html added in master a couple days ago do the job as far as your goal is concerned? (i.e. it reads all blocks ensuring they don't result in errrors). It is not multi-threaded per se. That said if your GeoTIFF is compressed and you specify "--config GDAL_NUM_THREADS=ALL_CPUS" then you'll get multi-threaded decompression, which should reach close to optimal performance.
January 9, 2026 at 5:39 PM
Reposted
mdsumner.bsky.social
I grew tired of searching "time now utc", please take a look at {timenow} #RStats

github.com/hypertidy/ti...

(thanks for the {clock} package by @davisvaughan.bsky.social !)
February 3, 2026 at 10:53 AM
Reposted
barneyharris.sciences.social.ap.brid.gy
#rstats #qgis #gischat blog post on layer blending with {tidyterra} https://barney.fly.dev/2026/01/27/ggplot2-blending-adventure/
My ggplot2 blending adventure | Reproducible Ruins
For my sins, I've gone all in on {ggplot2} as my static mapping library within R. Some years ago, I chose a serviceable path for my mapping needs, and then clun...
barney.fly.dev
January 29, 2026 at 8:33 AM
Reposted
hadley.nz
I love this idea: duckdb.org/community_ex.... It translates dplyr syntax _inside_ of duckdb so you can mix it with regular SQL
dplyr
DuckDB Community Extensions R dplyr pipeline syntax support for DuckDB - transpiles dplyr verbs to SQL
duckdb.org
January 27, 2026 at 7:08 PM
Reposted
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
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
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
Reposted
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
Reposted
delabj.bsky.social
Hey #rstats fam, is anyone else having issues with the new Pandas update and reticulate? It's not converting the pandas DataFrames to R for me on AWS SageMaker and I can't quite pin down why.
January 26, 2026 at 6:42 PM
Reposted
gmcd.bsky.social
Things are grim. But in more frivolous news...

@jamesbrandecon.bsky.social and I have been chipping away at `dbreg`, a 📦 for running big regression models on database backends. For the right kinds of problems, the speed-ups are near magical.

Website: grantmcdermott.com/dbreg/

#rstats

[1/2]
dbreg
grantmcdermott.com
January 26, 2026 at 4:57 PM
Reposted
josiah.rs
{b32} is now on CRAN!
Super speed base32 encoding & decoding compatible with tidyverse {blob} package (still 0️⃣ dependencies!)

#rstats
cran.r-project.org/web/packages...
b32: Fast and Vectorized Base32 Encoding
Fast, dependency free, and vectorized base32 encoding and decoding. 'b32' supports the Crockford, Z, RFC 4648 lower, hex, and lower hex alphabets.
cran.r-project.org
January 24, 2026 at 12:05 AM
Reposted
mdsumner.bsky.social
a new #GDAL backend for xarray, coupled directly for Multidim *and* Classic raster (and actually works, pretty good improv this week)

github.com/mdsumner/gdx

Please try it out with your most|least favourite Zarr! If you have connection issues just ask I know enough to be dangerous #python
GitHub - mdsumner/gdx: GDAL backend for xarray, enabling Classic or Multidim
GDAL backend for xarray, enabling Classic or Multidim - GitHub - mdsumner/gdx: GDAL backend for xarray, enabling Classic or Multidim
github.com
January 23, 2026 at 12:31 PM
hughagraham.bsky.social
New release is more stable and should avoid annoying false positive linting errors. 👍
January 23, 2026 at 1:34 PM
Reposted
etiennebacher.bsky.social
#rstats tidypolars 0.16.0 is available!

tidypolars provides the tidyverse syntax while using polars for better perf.

This release:
- support for unnest and separate functions (tidyr)
- new interface to export partitioned output
- and more

News: www.tidypolars.etiennebacher.com/news/#tidypo...
Changelog
www.tidypolars.etiennebacher.com
January 22, 2026 at 6:46 PM
Reposted
belian-earth.bsky.social
Climate Hub Davos. "How you interpret data is crucial to interpreting risk."

Everyone's building data products. Few are building the interpretation layer - Geospatial foundation models + causal inference + counterfactual baselines, not just maps.

Blog: belian.earth/news/davos-w...
Skiing Davos During WEF 2026: Nature on the Table at Climate Hub Davos
belian.earth at WEF 2026: empty slopes, full conversations. Reflections on carbon markets, nature credits, and the Climate Hub Davos.
belian.earth
January 22, 2026 at 12:47 PM
hughagraham.bsky.social
If you use #positron #rstats and #duckdb I'd love to know what you think of this:

`duckdb-r-editor` a Positron extension for duckdb SQL code highlighting and completion within R files.
github.com/belian-earth...
GitHub - belian-earth/duckdb-r-editor: A vscode extension to create a rich in-line SQL editor experience
A vscode extension to create a rich in-line SQL editor experience - belian-earth/duckdb-r-editor
github.com
January 22, 2026 at 10:23 AM
Reposted
juliasilge.com
The latest release of #Positron has a TOTAL REVAMP of the integration to GitHub Copilot, which solves a ton of auth problems!

In this screencast, I walk through how to set up Positron Assistant 🤖 to use GitHub Copilot as a model provider:

youtu.be/T8dCQ6iIFXo
Use GitHub Copilot with Positron Assistant
YouTube video by Julia Silge
youtu.be
January 20, 2026 at 2:34 PM
Reposted
belian-earth.bsky.social
#Restoration is seen as the safer bet for #carbon finance. But it faces the same baseline challenge as avoided deforestation.
Both require a defensible #counterfactual. We revisit a
@science.org paper five years on.

belian.earth/news/counter...

www.science.org/doi/10.1126/...

#forests
Forest Carbon Baselines: Why Counterfactual Analysis Matters for Carbon Credits
Scientific research on counterfactual baselines for forest carbon projects. How robust baseline estimation improves the credibility of carbon credits and offsets from restoration and avoided deforesta...
belian.earth
January 10, 2026 at 10:37 AM
Reposted
tterence.bsky.social
Nine volcanoes of Japan. Mt. Fuji is instantly recognisable. The others too, I hope.

This took a while to get right. Looks like fancy chocolates, no? Or little LED buttons.

#rayshader adventures, an #rstats tale
A visualisation of nine Japanese volcanoes
January 17, 2026 at 1:17 AM