SMT
@pp0196.bsky.social
Sequences and consequences.
Credit Pic : Cellular landscape cross-section through a eukaryotic cell, by Evan Ingersoll
Credit Pic : Cellular landscape cross-section through a eukaryotic cell, by Evan Ingersoll
Reposted by SMT
plinkQC: An Integrated Tool for Ancestry Inference, Sample Selection, and Quality Control in Population Genetics www.biorxiv.org/content/10.1... 🧬🖥️🧪 R package meyer-lab-cshl.github.io/plinkQC/ #Rstats
November 28, 2025 at 3:01 PM
plinkQC: An Integrated Tool for Ancestry Inference, Sample Selection, and Quality Control in Population Genetics www.biorxiv.org/content/10.1... 🧬🖥️🧪 R package meyer-lab-cshl.github.io/plinkQC/ #Rstats
Reposted by SMT
AI-Generated “Slop” in Online Biomedical Science Educational Videos: Mixed Methods Study of Prevalence, Characteristics, and Hazards to Learners and Teachers pmc.ncbi.nlm.nih.gov/articles/PMC... 🧬🖥️🧪
November 26, 2025 at 3:02 PM
AI-Generated “Slop” in Online Biomedical Science Educational Videos: Mixed Methods Study of Prevalence, Characteristics, and Hazards to Learners and Teachers pmc.ncbi.nlm.nih.gov/articles/PMC... 🧬🖥️🧪
Reposted by SMT
This is AMAZING! And it's so fantastic to see Fulgor helping out in these large-scale search tasks cc @jermp.bsky.social @ale-campa.bsky.social !
Optimized k-mer search across millions of bacterial genomes on laptops https://www.biorxiv.org/content/10.1101/2025.11.23.690050v1
November 26, 2025 at 5:52 PM
This is AMAZING! And it's so fantastic to see Fulgor helping out in these large-scale search tasks cc @jermp.bsky.social @ale-campa.bsky.social !
Reposted by SMT
Genome region aware CADD thresholds for noncoding variant prioritization academic.oup.com/nargab/artic... 🧬🖥️🧪
November 26, 2025 at 7:01 PM
Genome region aware CADD thresholds for noncoding variant prioritization academic.oup.com/nargab/artic... 🧬🖥️🧪
Simple #RStats Foreign Function interface using libffi, inspired by the Rffi package by Duncan T Lang. A fair amount of "conscious" memory leaks and experimention with S7 on my side. Despite the overhead compared to .Call, calling arbitrary C functions at runtime is nice.
github.com/sounkou-bioi...
github.com/sounkou-bioi...
November 27, 2025 at 1:33 AM
Simple #RStats Foreign Function interface using libffi, inspired by the Rffi package by Duncan T Lang. A fair amount of "conscious" memory leaks and experimention with S7 on my side. Despite the overhead compared to .Call, calling arbitrary C functions at runtime is nice.
github.com/sounkou-bioi...
github.com/sounkou-bioi...
Reposted by SMT
Thanks for the support of @caixaresearch.bsky.social to continue our efforts to use tissue engineering to study cerebral malaria. We will develop stem-cell derived immunocompetent BBB models with microglia to study malaria, in a side by side comparison with spatial transcriptomics in patients.
1/ Cerebral malaria is a severe form of malaria that causes damage to the blood vessels in the brain.
With a #HealthResearch grant, @mariabernabeu.bsky.social uses analytical techniques and human 3D models of blood vessels to ⬆️ our understanding and test new therapies.
https://tinyurl.com/2vtjnwn6
With a #HealthResearch grant, @mariabernabeu.bsky.social uses analytical techniques and human 3D models of blood vessels to ⬆️ our understanding and test new therapies.
https://tinyurl.com/2vtjnwn6
November 20, 2025 at 3:50 PM
Thanks for the support of @caixaresearch.bsky.social to continue our efforts to use tissue engineering to study cerebral malaria. We will develop stem-cell derived immunocompetent BBB models with microglia to study malaria, in a side by side comparison with spatial transcriptomics in patients.
Reposted by SMT
#rstats Please welcome Jarl, a new R linter.
Jarl is a CLI tool with extensions in VS Code, Positron, and Zed. It can check thousands of lines of R code in milliseconds.
Jarl provides several output formats, a Github Actions workflow, and more.
Blog post: www.etiennebacher.com/posts/2025-1...
Jarl is a CLI tool with extensions in VS Code, Positron, and Zed. It can check thousands of lines of R code in milliseconds.
Jarl provides several output formats, a Github Actions workflow, and more.
Blog post: www.etiennebacher.com/posts/2025-1...
November 20, 2025 at 4:50 PM
#rstats Please welcome Jarl, a new R linter.
Jarl is a CLI tool with extensions in VS Code, Positron, and Zed. It can check thousands of lines of R code in milliseconds.
Jarl provides several output formats, a Github Actions workflow, and more.
Blog post: www.etiennebacher.com/posts/2025-1...
Jarl is a CLI tool with extensions in VS Code, Positron, and Zed. It can check thousands of lines of R code in milliseconds.
Jarl provides several output formats, a Github Actions workflow, and more.
Blog post: www.etiennebacher.com/posts/2025-1...
Reposted by SMT
After years of working with Quarto, I've refined a set of editor settings that significantly improve document editing efficiency.
My latest blog post shares these battle-tested configurations.
mickael.canouil.fr/posts/2025-1...
#Quarto #VSCode #Positron #Productivity #DataScience
My latest blog post shares these battle-tested configurations.
mickael.canouil.fr/posts/2025-1...
#Quarto #VSCode #Positron #Productivity #DataScience
Optimising VS Code and Positron for Quarto: Essential Settings for Better Editing – MCU
Discover the custom settings I use in VS Code and Positron to enhance my Quarto document editing workflow, from improved Git diffs to better visual guides for nested divs.
mickael.canouil.fr
November 20, 2025 at 9:43 AM
After years of working with Quarto, I've refined a set of editor settings that significantly improve document editing efficiency.
My latest blog post shares these battle-tested configurations.
mickael.canouil.fr/posts/2025-1...
#Quarto #VSCode #Positron #Productivity #DataScience
My latest blog post shares these battle-tested configurations.
mickael.canouil.fr/posts/2025-1...
#Quarto #VSCode #Positron #Productivity #DataScience
Reposted by SMT
Remember to register for the first webinar in the new series “Towards a Human Exposome Cell Atlas”, held on Tuesday, 9 December. You can register at buff.ly/FfAYSCZ
🖥️ 🧬 #Exposome #Genomics #SingleCell
🖥️ 🧬 #Exposome #Genomics #SingleCell
November 20, 2025 at 12:05 PM
Remember to register for the first webinar in the new series “Towards a Human Exposome Cell Atlas”, held on Tuesday, 9 December. You can register at buff.ly/FfAYSCZ
🖥️ 🧬 #Exposome #Genomics #SingleCell
🖥️ 🧬 #Exposome #Genomics #SingleCell
Reposted by SMT
Capsule: Comprehensive Reproducibility Framework for R and Bioinformatics Workflows github.com/SAADAT-Abu/C... ...Generates Docker containers, exports to Nextflow & Snakemake #Rstats
November 19, 2025 at 7:02 PM
Capsule: Comprehensive Reproducibility Framework for R and Bioinformatics Workflows github.com/SAADAT-Abu/C... ...Generates Docker containers, exports to Nextflow & Snakemake #Rstats
Reposted by SMT
Just published in Research Synthesis Methods
How to be more accurate than humans at abstract screening tasks using several small open-weight LLM?
doi.org/10.1017/rsm....
We actually circumvented the "LLM lie and hallucinate" problem for simple text analysis tasks !!
Let me explain
⬇️1/8
How to be more accurate than humans at abstract screening tasks using several small open-weight LLM?
doi.org/10.1017/rsm....
We actually circumvented the "LLM lie and hallucinate" problem for simple text analysis tasks !!
Let me explain
⬇️1/8
Beyond human gold standards: A multimodel framework for automated abstract classification and information extraction | Research Synthesis Methods | Cambridge Core
Beyond human gold standards: A multimodel framework for automated abstract classification and information extraction
doi.org
November 18, 2025 at 9:30 AM
Just published in Research Synthesis Methods
How to be more accurate than humans at abstract screening tasks using several small open-weight LLM?
doi.org/10.1017/rsm....
We actually circumvented the "LLM lie and hallucinate" problem for simple text analysis tasks !!
Let me explain
⬇️1/8
How to be more accurate than humans at abstract screening tasks using several small open-weight LLM?
doi.org/10.1017/rsm....
We actually circumvented the "LLM lie and hallucinate" problem for simple text analysis tasks !!
Let me explain
⬇️1/8
R(r)ustaceans out there, please give us a #wasm runtime within #Rstats, I said khalas after 5 hours of vibecoding this 😂 (my bad, I should have gone for a pure C wasm runtime library, at least there I can read the header files). All of this for faster fibonacci 😂
github.com/sounkou-bioi...
github.com/sounkou-bioi...
November 19, 2025 at 2:28 AM
R(r)ustaceans out there, please give us a #wasm runtime within #Rstats, I said khalas after 5 hours of vibecoding this 😂 (my bad, I should have gone for a pure C wasm runtime library, at least there I can read the header files). All of this for faster fibonacci 😂
github.com/sounkou-bioi...
github.com/sounkou-bioi...
#Rstats gurus
do we have tools to respond to this idea from john chambers ?
""" If not, can the non-functionality be
parametrized... ? R
does not have organized support for such validity
investigations, but developing tools for the purpose
would be a worthwhile project."""
arxiv.org/pdf/1409.3531
do we have tools to respond to this idea from john chambers ?
""" If not, can the non-functionality be
parametrized... ? R
does not have organized support for such validity
investigations, but developing tools for the purpose
would be a worthwhile project."""
arxiv.org/pdf/1409.3531
November 18, 2025 at 11:59 AM
#Rstats gurus
do we have tools to respond to this idea from john chambers ?
""" If not, can the non-functionality be
parametrized... ? R
does not have organized support for such validity
investigations, but developing tools for the purpose
would be a worthwhile project."""
arxiv.org/pdf/1409.3531
do we have tools to respond to this idea from john chambers ?
""" If not, can the non-functionality be
parametrized... ? R
does not have organized support for such validity
investigations, but developing tools for the purpose
would be a worthwhile project."""
arxiv.org/pdf/1409.3531
Reposted by SMT
I recently discovered Conventional Comments (conventionalcomments.org) for providing a pseudo-standard set of labels for feedback and just tried it for an article review and it was really helpful to specify issues vs. thoughts vs. suggestions, etc. Hopefully it's helpful for the authors too!
November 17, 2025 at 3:52 PM
I recently discovered Conventional Comments (conventionalcomments.org) for providing a pseudo-standard set of labels for feedback and just tried it for an article review and it was really helpful to specify issues vs. thoughts vs. suggestions, etc. Hopefully it's helpful for the authors too!
Reposted by SMT
🔥 {torchgnn} 🕸️ is a WIP implementation of Graph Neural Networks in R.
- GCN
- GCN (generalized)
- GraphSAGE
- Aggregators
Development based on personal needs, ofc :)
#rstats
github.com/JosiahParry/...
- GCN
- GCN (generalized)
- GraphSAGE
- Aggregators
Development based on personal needs, ofc :)
#rstats
github.com/JosiahParry/...
November 13, 2025 at 8:14 PM
🔥 {torchgnn} 🕸️ is a WIP implementation of Graph Neural Networks in R.
- GCN
- GCN (generalized)
- GraphSAGE
- Aggregators
Development based on personal needs, ofc :)
#rstats
github.com/JosiahParry/...
- GCN
- GCN (generalized)
- GraphSAGE
- Aggregators
Development based on personal needs, ofc :)
#rstats
github.com/JosiahParry/...
Reposted by SMT
November 2025 WikiPathways update: 686 edits by 6 contributors and 10 new pathways in the last month. Accessible via #webservices, #rstats, #PathVisio and #Cytoscape.
Supported by #AWSOpen. https://www.wikipathways.org/index.php/Download_Pathways
#bioinformatics #openscience #opensource
Supported by #AWSOpen. https://www.wikipathways.org/index.php/Download_Pathways
#bioinformatics #openscience #opensource
November 12, 2025 at 6:21 AM
November 2025 WikiPathways update: 686 edits by 6 contributors and 10 new pathways in the last month. Accessible via #webservices, #rstats, #PathVisio and #Cytoscape.
Supported by #AWSOpen. https://www.wikipathways.org/index.php/Download_Pathways
#bioinformatics #openscience #opensource
Supported by #AWSOpen. https://www.wikipathways.org/index.php/Download_Pathways
#bioinformatics #openscience #opensource
Sustainable and effective vibe coding requires good taste and that taste is definitely not going to be acquired through vibe coding.
I guess it also helps that you vibe code in a language with good baseline taste in the training sets like #Rstats of course (^_^)
I guess it also helps that you vibe code in a language with good baseline taste in the training sets like #Rstats of course (^_^)
November 7, 2025 at 9:00 PM
Sustainable and effective vibe coding requires good taste and that taste is definitely not going to be acquired through vibe coding.
I guess it also helps that you vibe code in a language with good baseline taste in the training sets like #Rstats of course (^_^)
I guess it also helps that you vibe code in a language with good baseline taste in the training sets like #Rstats of course (^_^)
Reposted by SMT
I put out a patch release of mirai today. Version 2.5.2 really improves the OpenTelemetry integration so you can more easily see into your async workflows. Other key ecosystem packages will roll out with this enabled - next up: Shiny!
mirai.r-lib.org
#Rstats
mirai.r-lib.org
#Rstats
Minimalist Async Evaluation Framework for R
Designed for simplicity, a mirai evaluates an R expression asynchronously, locally or distributed over the network. Built on nanonext and NNG for modern networking and concurrency, scales efficiently ...
mirai.r-lib.org
November 5, 2025 at 10:37 PM
I put out a patch release of mirai today. Version 2.5.2 really improves the OpenTelemetry integration so you can more easily see into your async workflows. Other key ecosystem packages will roll out with this enabled - next up: Shiny!
mirai.r-lib.org
#Rstats
mirai.r-lib.org
#Rstats
Reposted by SMT
We recently checked out tidySingleCellExperiment at the R Stats Club @libdrstats.bsky.social, an R package part of a broader effort to bring tidy coding to genomics. Pretty useful!
youtu.be/ob_SQY4-YjQ?...
#RStats
youtu.be/ob_SQY4-YjQ?...
#RStats
[2025-07-11] Tidy manipulation of SingleCellExperiment objects
YouTube video by Leonardo Collado Torres
youtu.be
November 4, 2025 at 4:09 PM
We recently checked out tidySingleCellExperiment at the R Stats Club @libdrstats.bsky.social, an R package part of a broader effort to bring tidy coding to genomics. Pretty useful!
youtu.be/ob_SQY4-YjQ?...
#RStats
youtu.be/ob_SQY4-YjQ?...
#RStats
As it happens, there is a R level equivalent of the C API finalization registration mechanism stat.ethz.ch/R-manual/R-d...
Never saw it in the wild, but it looks like some CRAN packages use it (expectedly lot of these packages manage external processes)
github.com/search?q=org...
#Rstats
Never saw it in the wild, but it looks like some CRAN packages use it (expectedly lot of these packages manage external processes)
github.com/search?q=org...
#Rstats
R: Finalization of Objects
stat.ethz.ch
November 3, 2025 at 5:10 PM
As it happens, there is a R level equivalent of the C API finalization registration mechanism stat.ethz.ch/R-manual/R-d...
Never saw it in the wild, but it looks like some CRAN packages use it (expectedly lot of these packages manage external processes)
github.com/search?q=org...
#Rstats
Never saw it in the wild, but it looks like some CRAN packages use it (expectedly lot of these packages manage external processes)
github.com/search?q=org...
#Rstats
Use any python library and you quickly find yourself buried under layers upon layers of encapsulated OOP inheritance crap, the tracebacks are order of magnitude worse than tidyverse NSE tracebacks before the rlang package (this is when the module author allows you to see traces)
November 3, 2025 at 3:50 PM
Use any python library and you quickly find yourself buried under layers upon layers of encapsulated OOP inheritance crap, the tracebacks are order of magnitude worse than tidyverse NSE tracebacks before the rlang package (this is when the module author allows you to see traces)
Reposted by SMT
R version 4.5.2 "[Not] Part in a Rumble" (source version) has been released. (You can find it in cran.r-project.org/src/base/R-4/, or wait for CRAN to be updated.)
October 31, 2025 at 9:44 AM
R version 4.5.2 "[Not] Part in a Rumble" (source version) has been released. (You can find it in cran.r-project.org/src/base/R-4/, or wait for CRAN to be updated.)
Reposted by SMT
luz v0.5.1 is now on #rstats CRAN. Just a small bug fix related to forwarding `predict` parameters to the model. I also added a new Variational Autoencoder example to our examples gallery: mlverse.github.io/luz/articles...
Examples
mlverse.github.io
October 30, 2025 at 12:52 PM
luz v0.5.1 is now on #rstats CRAN. Just a small bug fix related to forwarding `predict` parameters to the model. I also added a new Variational Autoencoder example to our examples gallery: mlverse.github.io/luz/articles...