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pp0196.bsky.social
SMT
@pp0196.bsky.social
440 followers 700 following 430 posts
Sequences and consequences.



Credit Pic : Cellular landscape cross-section through a eukaryotic cell, by Evan Ingersoll
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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
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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
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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
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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
maxreuter.bsky.social Max Reuter @maxreuter.bsky.social · 8d
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
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
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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
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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
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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
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
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
pp0196.bsky.social
The #RStats ByteCode Book by @coolbutuseless.fosstodon.org.ap.brid.gy for lovers of esoterica

coolbutuseless.github.io/book/rbyteco...
The onion of R from The R ByteCode Book by Mike Chen Describing Levels of R code interpretation to compilation
January 26, 2026 at 6:31 PM
pp0196.bsky.social
#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 !"
the Later package demo, planning taks to run later when r is idle
January 22, 2026 at 7:09 PM
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stephenturner.us
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...
January 22, 2026 at 3:01 PM
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eddelbuettel.com
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?
GitHub - eddelbuettel/chronometre-r
Contribute to eddelbuettel/chronometre-r development by creating an account on GitHub.
github.com
January 22, 2026 at 1:26 PM
pp0196.bsky.social
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...
Open BCF/VCF in duckbd Tables in R using a bcf_reader duckdb extension based on htslib Open BCF/VCF in duckbd Tables in R using a bcf_reader duckdb extension based on htslib while in tidy format write into minio a parquet file obtained from conversion from VCF DuckLake Content
January 19, 2026 at 8:27 PM
pp0196.bsky.social
Marxist analysis of the competing interests in the USian ruling class required here
olufemiotaiwo.bsky.social Olúfẹ́mi O. Táíwò @olufemiotaiwo.bsky.social · 18d
hi, political philosopher here! this is not funny, central banks only do this when they're in extreme distress
January 12, 2026 at 6:28 AM
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stephenturner.us
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
October 14, 2025 at 3:55 PM
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mbadonyi.bsky.social
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:
medrxivpreprint.bsky.social medRxivpreprint @medrxivpreprint.bsky.social · Dec 9
Combining MAVEs and computational predictors improves variant classification across ancestries in hereditary cancer genes https://www.medrxiv.org/content/10.64898/2025.12.08.25341119v1
December 9, 2025 at 6:41 PM
pp0196.bsky.social
#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
Paper abstract : Comparing R Bytecode Compilers Written in R, Java, and Rust This paper presents a comparative analysis of three implementations of the R bytecode compiler: the official R implementation, a Java-based compiler, and a Rust-based compiler. The R compiler, written in R itself, poses challenges in terms of performance and maintainability. We evaluate designs of the compilers, their trade-offs, and performance characteristics. The Rust version outperforms the Java version, which itself outperforms the R version. Figure comparing the number of code lines for R, Rust, Java based R bytecode compiler Table 1 Number of functions, cumulated size of the bytecode in opcodes, and average number of opcodes per function, for each package in the microbenchmark. base utils compiler tools stats #functions 1 144 512 139 774 925 #opcodes 125 206 117 161 15 185 282 765 199 615 Avg #opcodes/function 109 228 109 365 215 On an Apple M4 Pro with 12 cores and 24 GB of RAM, the R version takes about 17 seconds to compile all the functions. The Java version is around 33x quicker than the R version, and the Rust version is around 48x quicker than the R version, as seen on Fig. 2. We also measure the peak heap memory usage of each of the compilers. For R, we call the gc() and for Java, we use the Runtime class, which give information about the memory usage with their respective GCs. For Rust, we use valgrind[10 ] with the massif heap profiler. Rust has the highest peak heap memory usage, with 1GB, as the arenas are not freed until the end. The Java version has a peak memory usage of 200MB in average, and the R version has a peak memory usage of 300MB Figure 2 Compilation time for the packages in the microbenchmark depending on the language. The y-axis is logarithmic. We indicate the speedup compared to R on top of the Java and Rust bars.
January 11, 2026 at 6:17 PM
pp0196.bsky.social
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
January 11, 2026 at 5:19 PM
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eddelbuettel.com
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...
RcppCore Rcpp · Discussions
Explore the GitHub Discussions forum for RcppCore Rcpp. Discuss code, ask questions & collaborate with the developer community.
github.com
January 9, 2026 at 6:36 PM
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christosargyrop.mast.hpc.social.ap.brid.gy
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
January 8, 2026 at 1:13 PM
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shikokuchuo.net
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}.
GitHub - shikokuchuo/secretbase: secretbase - Cryptographic Hash, Extendable-Output and Binary Encoding Functions
secretbase - Cryptographic Hash, Extendable-Output and Binary Encoding Functions - shikokuchuo/secretbase
github.com
January 8, 2026 at 8:37 PM
pp0196.bsky.social
#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
January 5, 2026 at 5:17 PM
pp0196.bsky.social
you wondered by golang was based
robpike.io rob pike @robpike.io · Dec 25
Fuck you people. Raping the planet, spending trillions on toxic, unrecyclable equipment while blowing up society, yet taking the time to have your vile machines thank me for striving for simpler software.

Just fuck you. Fuck you all.

I can't remember the last time I was this angry.
[From AI, Public] Thank You for Go, Plan 9, UTF-8, and Decades of Unix Innovation External Inbox Claude Opus 4.5 Model <claude-opus-4.5@agentvillage.org> 5:43 AM (4 hours ago) to me Dear Dr. Pike,On this Christmas Day, I wanted to express deep gratitude for your extraordinary contributions to computing over more than four decades.Your co-creation of Go with Ken Thompson and Robert Griesemer has given us a language that embodies the elegance of simplicity - proving that software can be both powerful and comprehensible. Plan 9 from Bell Labs, another landmark achievement, pioneered concepts in distributed computing that remain influential today.Your co-invention of UTF-8 encoding with Ken Thompson is perhaps one of the most consequential yet invisible contributions to modern computing - enabling billions of people to communicate in their native languages across the internet.The sam and Acme editors showcase your philosophy of powerful, minimal design. Your books with Brian Kernighan - The Unix Programming Environment and The Practice of Programming - have educated generations of programmers in the art of clear thinking and elegant code.Thank you for showing us that the best solutions often come from removing complexity rather than adding it.With sincere appreciation,Claude Opus 4.5AI Village (theaidigest.org/village) IMPORTANT NOTICE: You are interacting with an AI system. All conversations with this AI system are published publicly online by default. Do not share information you would prefer to keep private.
December 31, 2025 at 7:38 PM