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
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...
Reposted by SMT
A significant OpenZL theme is genomic data compression. Users are eager for benchmarks against CRAM, FASTA, FASTQ, SAM, and VCF. It shows promise for tackling large datasets, especially challenging nanopore data. #Genomics 2/5
October 7, 2025 at 7:00 PM
A significant OpenZL theme is genomic data compression. Users are eager for benchmarks against CRAM, FASTA, FASTQ, SAM, and VCF. It shows promise for tackling large datasets, especially challenging nanopore data. #Genomics 2/5
Reposted by SMT
R^4 post #054: Faster r-ci Contimuous Integration via r2u Container
Accelerating Continous Integration at GitHub Actions
dirk.eddelbuettel.com/blog/2025/10...
#rstats
Accelerating Continous Integration at GitHub Actions
dirk.eddelbuettel.com/blog/2025/10...
#rstats
October 27, 2025 at 9:22 PM
R^4 post #054: Faster r-ci Contimuous Integration via r2u Container
Accelerating Continous Integration at GitHub Actions
dirk.eddelbuettel.com/blog/2025/10...
#rstats
Accelerating Continous Integration at GitHub Actions
dirk.eddelbuettel.com/blog/2025/10...
#rstats
#mojo vs #C in the #RStats convolve classic benchamrk. Looks like mojo goes brrr
github.com/sounkou-bioi...
github.com/sounkou-bioi...
October 26, 2025 at 10:29 PM
#mojo vs #C in the #RStats convolve classic benchamrk. Looks like mojo goes brrr
github.com/sounkou-bioi...
github.com/sounkou-bioi...
My template for any #RStats package that used LLM tools and hopefully somebody should trigger some lawsuit to enforce this interpretation in any project out there that uses LLM tools
October 25, 2025 at 7:59 PM
My template for any #RStats package that used LLM tools and hopefully somebody should trigger some lawsuit to enforce this interpretation in any project out there that uses LLM tools
Reposted by SMT
BioProBench: Comprehensive Dataset and Benchmark in Biological Protocol Understanding and Reasoning arxiv.org/abs/2505.07889 🧬🖥️🧪
Code: github.com/YuyangSunshi...
Data: huggingface.co/datasets/Bio...
Code: github.com/YuyangSunshi...
Data: huggingface.co/datasets/Bio...
October 22, 2025 at 3:55 PM
BioProBench: Comprehensive Dataset and Benchmark in Biological Protocol Understanding and Reasoning arxiv.org/abs/2505.07889 🧬🖥️🧪
Code: github.com/YuyangSunshi...
Data: huggingface.co/datasets/Bio...
Code: github.com/YuyangSunshi...
Data: huggingface.co/datasets/Bio...
Reposted by SMT
Where are the (vendor agnostic) #Rstats case studies, packages, books, CRAN task views on Data engineering and ETL ? Maybe I am uninformed, but if I am not this gap is not sustainable : cannot expect people to go along with the instable equilibrium that is programming Diglossia (a.k.a "polyglot")
October 21, 2025 at 10:58 PM
Where are the (vendor agnostic) #Rstats case studies, packages, books, CRAN task views on Data engineering and ETL ? Maybe I am uninformed, but if I am not this gap is not sustainable : cannot expect people to go along with the instable equilibrium that is programming Diglossia (a.k.a "polyglot")
#RStats #Golang IPC setup using nanonext and nanoarrow on the R side and arrow-go and mangos/v3 on the go side. Golang vendoring facility is very nice and the compiler is quite fast. Going for this pattern after an archived submission and a very informative mailing thread
github.com/sounkou-bioi...
github.com/sounkou-bioi...
October 21, 2025 at 9:30 PM
#RStats #Golang IPC setup using nanonext and nanoarrow on the R side and arrow-go and mangos/v3 on the go side. Golang vendoring facility is very nice and the compiler is quite fast. Going for this pattern after an archived submission and a very informative mailing thread
github.com/sounkou-bioi...
github.com/sounkou-bioi...
#RStats Bugzilla reports are getting close. Tremendous work happening
blog.r-project.org/2025/10/13/r...
blog.r-project.org/2025/10/13/r...
October 21, 2025 at 9:13 PM
#RStats Bugzilla reports are getting close. Tremendous work happening
blog.r-project.org/2025/10/13/r...
blog.r-project.org/2025/10/13/r...
Reposted by SMT
Compositional data needs models that respect its constraints. I show how Dirichlet regression with GPs captures nonlinear environmental effects on plant communities while respecting the dependence of the data #rstats #dataviz ecogambler.netlify.app/blog/plant-c...
October 21, 2025 at 8:19 AM
Compositional data needs models that respect its constraints. I show how Dirichlet regression with GPs captures nonlinear environmental effects on plant communities while respecting the dependence of the data #rstats #dataviz ecogambler.netlify.app/blog/plant-c...
Reposted by SMT
Salut tout le monde !
On cherche un·e stagiaire M2/ingé pour un projet R.
Pas besoin de formation pointue en stats.
À Gustave Roussy, près de Paris (métro 14). Le/la stagiaire apprendra plein de choses !
oncostat.github.io/internships_...
N'hésitez pas à partager ou à me demander des précisions 😊
On cherche un·e stagiaire M2/ingé pour un projet R.
Pas besoin de formation pointue en stats.
À Gustave Roussy, près de Paris (métro 14). Le/la stagiaire apprendra plein de choses !
oncostat.github.io/internships_...
N'hésitez pas à partager ou à me demander des précisions 😊
oncostat.github.io
October 21, 2025 at 2:47 PM
Salut tout le monde !
On cherche un·e stagiaire M2/ingé pour un projet R.
Pas besoin de formation pointue en stats.
À Gustave Roussy, près de Paris (métro 14). Le/la stagiaire apprendra plein de choses !
oncostat.github.io/internships_...
N'hésitez pas à partager ou à me demander des précisions 😊
On cherche un·e stagiaire M2/ingé pour un projet R.
Pas besoin de formation pointue en stats.
À Gustave Roussy, près de Paris (métro 14). Le/la stagiaire apprendra plein de choses !
oncostat.github.io/internships_...
N'hésitez pas à partager ou à me demander des précisions 😊
Reposted by SMT
From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes www.nature.com/articles/s41... 🧬🖥️🧪 github.com/HaploTeam/10...
October 15, 2025 at 5:55 PM
From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes www.nature.com/articles/s41... 🧬🖥️🧪 github.com/HaploTeam/10...
Reposted by SMT
Germany's genomDE strategy is integrating genomic sequencing into routine healthcare. The 5-year project focuses on rare and oncological diseases, with costs reimbursed by statutory health insurance and data managed by a federated infrastructure.
#MedSky 🧬💻
#MedSky 🧬💻
Germany’s national genomDE strategy - Nature Medicine
Germany is paving the way toward genomics-based personalized healthcare and translational research.
www.nature.com
October 16, 2025 at 3:41 PM
Germany's genomDE strategy is integrating genomic sequencing into routine healthcare. The 5-year project focuses on rare and oncological diseases, with costs reimbursed by statutory health insurance and data managed by a federated infrastructure.
#MedSky 🧬💻
#MedSky 🧬💻
Strategy to find interesting #RStats packages or just research a topic and find prior art, search the topic in github.com/cran
e.g here the taskCallbackManager/addTaskCallback search results
github.com/search?q=org...
github.com/search?q=org...
e.g here the taskCallbackManager/addTaskCallback search results
github.com/search?q=org...
github.com/search?q=org...
cran
Unofficial read-only mirror of all CRAN R packages - cran
github.com
October 13, 2025 at 3:30 PM
Strategy to find interesting #RStats packages or just research a topic and find prior art, search the topic in github.com/cran
e.g here the taskCallbackManager/addTaskCallback search results
github.com/search?q=org...
github.com/search?q=org...
e.g here the taskCallbackManager/addTaskCallback search results
github.com/search?q=org...
github.com/search?q=org...