The latest issue of @rweekly is live!
https://rweekly.org/2026-W38.html
The week's highlights:
🔪 Slicing in tidyomics by @mikelove
⚠️ Prevent accidental many-to-many joins in R with synthetic sports odds by Jacob Galperin
⚛️ Positron September Release Highlights by @juliasilge
As always […]
https://rweekly.org/2026-W38.html
The week's highlights:
🔪 Slicing in tidyomics by @mikelove
⚠️ Prevent accidental many-to-many joins in R with synthetic sports odds by Jacob Galperin
⚛️ Positron September Release Highlights by @juliasilge
As always […]
Original post on fosstodon.org
fosstodon.org
September 14, 2026 at 12:09 PM
The latest issue of @rweekly is live!
https://rweekly.org/2026-W38.html
The week's highlights:
🔪 Slicing in tidyomics by @mikelove
⚠️ Prevent accidental many-to-many joins in R with synthetic sports odds by Jacob Galperin
⚛️ Positron September Release Highlights by @juliasilge
As always […]
https://rweekly.org/2026-W38.html
The week's highlights:
🔪 Slicing in tidyomics by @mikelove
⚠️ Prevent accidental many-to-many joins in R with synthetic sports odds by Jacob Galperin
⚛️ Positron September Release Highlights by @juliasilge
As always […]
I wrote a post about how slice_sample() and other slice_* functions work in #tidyomics #Bioconductor
tidyomics.github.io/tidyomicsBlo...
tidyomics.github.io/tidyomicsBlo...
September 12, 2026 at 4:05 PM
I wrote a post about how slice_sample() and other slice_* functions work in #tidyomics #Bioconductor
tidyomics.github.io/tidyomicsBlo...
tidyomics.github.io/tidyomicsBlo...
is happy to be at #useR2025. So far, I ran into 3 colleagues from various ventures, and learned
* how to underline text in Quarto markdown
* that a `countdown` can end with a sound effect
(in addition to a couple of great workshops about tidyomics and srvyr)
* how to underline text in Quarto markdown
* that a `countdown` can end with a sound effect
(in addition to a couple of great workshops about tidyomics and srvyr)
August 9, 2025 at 1:11 AM
is happy to be at #useR2025. So far, I ran into 3 colleagues from various ventures, and learned
* how to underline text in Quarto markdown
* that a `countdown` can end with a sound effect
(in addition to a couple of great workshops about tidyomics and srvyr)
* how to underline text in Quarto markdown
* that a `countdown` can end with a sound effect
(in addition to a couple of great workshops about tidyomics and srvyr)
Great to see a #EuroBioC2026 hackathon project sharing plans 👏
Tidyomics team outline what participants can get involved in.
Tidyomics team outline what participants can get involved in.
First #tidyomics hackathon at #EuroBioC2026 in Turku!
tidyomics.github.io/tidyomicsBlo...
Join us at Euro Bioc (eurobioc2026.bioconductor.org) for a dive into our ecosystem, where you can learn about it and, hands-on, improve and extend it.
Plz share! 🙏
@bioconductor.bsky.social
tidyomics.github.io/tidyomicsBlo...
Join us at Euro Bioc (eurobioc2026.bioconductor.org) for a dive into our ecosystem, where you can learn about it and, hands-on, improve and extend it.
Plz share! 🙏
@bioconductor.bsky.social
EuroBioC2026 Tidyomics Hackathon – tidyomicsBlog
An invitation to join the Tidyomics community hackathon at EuroBioC2026 in Turku, Finland.
tidyomics.github.io
May 31, 2026 at 8:20 AM
Great to see a #EuroBioC2026 hackathon project sharing plans 👏
Tidyomics team outline what participants can get involved in.
Tidyomics team outline what participants can get involved in.
📅 Tidyomics next meeting is Wed, Mar 12 at 4PM NY / 9PM London / 8AM (Thurs) Melbourne. They'll discuss enhancing SummarizedExperiment display & seek feedback on tidyprint package. See Bioconductor Slack #tidiness-in-bioc channel or events calendar for more info: buff.ly/rdhL3jL
#Tidyomics #RStats
#Tidyomics #RStats
Bioconductor - Events
The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and…
buff.ly
March 4, 2025 at 3:58 PM
📅 Tidyomics next meeting is Wed, Mar 12 at 4PM NY / 9PM London / 8AM (Thurs) Melbourne. They'll discuss enhancing SummarizedExperiment display & seek feedback on tidyprint package. See Bioconductor Slack #tidiness-in-bioc channel or events calendar for more info: buff.ly/rdhL3jL
#Tidyomics #RStats
#Tidyomics #RStats
@mikelove.bsky.social — the tidyomics paper is awesome! One nit; you forgot to include Rust in your hierarchy of languages (but it's the best one ;P).
September 14, 2023 at 5:23 PM
@mikelove.bsky.social — the tidyomics paper is awesome! One nit; you forgot to include Rust in your hierarchy of languages (but it's the best one ;P).
"Maintaining and refining the Tidyomics ecosystem: enhancing core packages and interoperability for EuroBioc2026" https://doi.org/10.37044/osf.io/cd9s6_v1
"First, we introduce tidyAnnData, a new package that expands interoperability between the tidyverse and […]
[Original post on fediscience.org]
"First, we introduce tidyAnnData, a new package that expands interoperability between the tidyverse and […]
[Original post on fediscience.org]
July 10, 2026 at 5:20 PM
"Maintaining and refining the Tidyomics ecosystem: enhancing core packages and interoperability for EuroBioc2026" https://doi.org/10.37044/osf.io/cd9s6_v1
"First, we introduce tidyAnnData, a new package that expands interoperability between the tidyverse and […]
[Original post on fediscience.org]
"First, we introduce tidyAnnData, a new package that expands interoperability between the tidyverse and […]
[Original post on fediscience.org]
Weekly recap: Bioconductor on GPUs, tidyomics, Quarto 1.8, Anthropic red-teaming on AIxBio, PGS in the clinic, Shock Doctrine in genome engineering, GenAI for data viz with #Rstats, Datapalooza, 4 compact rejections, more... blog.stephenturner.us/p/weekly-rec... 🧬🖥️🧪
October 17, 2025 at 12:41 PM
Weekly recap: Bioconductor on GPUs, tidyomics, Quarto 1.8, Anthropic red-teaming on AIxBio, PGS in the clinic, Shock Doctrine in genome engineering, GenAI for data viz with #Rstats, Datapalooza, 4 compact rejections, more... blog.stephenturner.us/p/weekly-rec... 🧬🖥️🧪
The tidyomics ecosystem: Enhancing omic data analyses https://www.biorxiv.org/content/10.1101/2023.09.10.557072v1
The tidyomics ecosystem: Enhancing omic data analyses https://www.biorxiv.org/content/10.1101/2023.09.10.557072v1
The exponential growth of omic data presents challenges in data manipulation, analysis, and integrat
www.biorxiv.org
September 14, 2023 at 4:00 AM
The tidyomics ecosystem: Enhancing omic data analyses https://www.biorxiv.org/content/10.1101/2023.09.10.557072v1
🚀 The 3rd edition of #SpatialOmics in #Rstats & @bioconductor.bsky.social with @stemang.bsky.social is officially underway!
Over the next 3 days: spatial DE, imaging & sequencing workflows, deconvolution, cell-neighbour analysis & multi-modal integration across Bioconductor, Seurat & tidyomics ✨
Over the next 3 days: spatial DE, imaging & sequencing workflows, deconvolution, cell-neighbour analysis & multi-modal integration across Bioconductor, Seurat & tidyomics ✨
May 18, 2026 at 9:46 AM
🚀 The 3rd edition of #SpatialOmics in #Rstats & @bioconductor.bsky.social with @stemang.bsky.social is officially underway!
Over the next 3 days: spatial DE, imaging & sequencing workflows, deconvolution, cell-neighbour analysis & multi-modal integration across Bioconductor, Seurat & tidyomics ✨
Over the next 3 days: spatial DE, imaging & sequencing workflows, deconvolution, cell-neighbour analysis & multi-modal integration across Bioconductor, Seurat & tidyomics ✨
The hands-on sessions of the course were built around the tidyomics ecosystem, a powerful framework that bridges Bioconductor and the tidyverse for streamlined omics data manipulation and analysis www.nature.com/articles/s41...
The tidyomics ecosystem: enhancing omic data analyses - Nature Methods
tidyomics offers a software ecosystem for omic data manipulation and analysis that bridges Bioconductor with the tidyverse framework.
www.nature.com
May 21, 2025 at 8:10 AM
The hands-on sessions of the course were built around the tidyomics ecosystem, a powerful framework that bridges Bioconductor and the tidyverse for streamlined omics data manipulation and analysis www.nature.com/articles/s41...
#TidyOmics
Harmonizing different omics packages with a common R syntax/grammar
tidySpatialExperiment "provides specialized operations such as gating based on geometric & hand-drawn shapes"😍
#NatureMethods 2024
www.nature.com/articles/s41...
Harmonizing different omics packages with a common R syntax/grammar
tidySpatialExperiment "provides specialized operations such as gating based on geometric & hand-drawn shapes"😍
#NatureMethods 2024
www.nature.com/articles/s41...
June 22, 2024 at 11:58 AM
#TidyOmics
Harmonizing different omics packages with a common R syntax/grammar
tidySpatialExperiment "provides specialized operations such as gating based on geometric & hand-drawn shapes"😍
#NatureMethods 2024
www.nature.com/articles/s41...
Harmonizing different omics packages with a common R syntax/grammar
tidySpatialExperiment "provides specialized operations such as gating based on geometric & hand-drawn shapes"😍
#NatureMethods 2024
www.nature.com/articles/s41...
The tidyomics map reminds of Brixen, location of the CSAMA summer schools.
(Participants will recognise Woody Walk, Plosehütte and Rossalm, destinations of the midweek course hike.)
(Participants will recognise Woody Walk, Plosehütte and Rossalm, destinations of the midweek course hike.)
October 23, 2025 at 11:29 AM
The tidyomics map reminds of Brixen, location of the CSAMA summer schools.
(Participants will recognise Woody Walk, Plosehütte and Rossalm, destinations of the midweek course hike.)
(Participants will recognise Woody Walk, Plosehütte and Rossalm, destinations of the midweek course hike.)
slice_sample() is especially useful for omics, with random sampling of cells or genomic regions, and arguments `prop` (proportion in [0,1]) and `weight_by` for weighted sampling.
slice_*() functions can be combined with grouping operations. I plan to write up examples for the tidyomics blog soon.
slice_*() functions can be combined with grouping operations. I plan to write up examples for the tidyomics blog soon.
May 3, 2026 at 8:38 PM
slice_sample() is especially useful for omics, with random sampling of cells or genomic regions, and arguments `prop` (proportion in [0,1]) and `weight_by` for weighted sampling.
slice_*() functions can be combined with grouping operations. I plan to write up examples for the tidyomics blog soon.
slice_*() functions can be combined with grouping operations. I plan to write up examples for the tidyomics blog soon.
Another Bioc 3.23 update: new dplyr function support for a number of tidyomics packages @stemang.bsky.social
Adding slice_sample, *_head, *_tail, *_min, and *_max to:
- tidySingleCellExperiment
- tidySeurat
- plyranges
The dplyr descriptions for these:
dplyr.tidyverse.org/reference/sl...
Adding slice_sample, *_head, *_tail, *_min, and *_max to:
- tidySingleCellExperiment
- tidySeurat
- plyranges
The dplyr descriptions for these:
dplyr.tidyverse.org/reference/sl...
May 3, 2026 at 8:35 PM
Another Bioc 3.23 update: new dplyr function support for a number of tidyomics packages @stemang.bsky.social
Adding slice_sample, *_head, *_tail, *_min, and *_max to:
- tidySingleCellExperiment
- tidySeurat
- plyranges
The dplyr descriptions for these:
dplyr.tidyverse.org/reference/sl...
Adding slice_sample, *_head, *_tail, *_min, and *_max to:
- tidySingleCellExperiment
- tidySeurat
- plyranges
The dplyr descriptions for these:
dplyr.tidyverse.org/reference/sl...
Let us know, e.g. @stemang.bsky.social or I if you have any ideas for something to post re: use cases for tidyomics to share or to develop.
December 8, 2025 at 5:29 PM
Let us know, e.g. @stemang.bsky.social or I if you have any ideas for something to post re: use cases for tidyomics to share or to develop.
tidyomics project 🔛 R-bloggers!
www.r-bloggers.com/2025/10/the-...
Thanks to @stemang.bsky.social, Maria Doyle @bioconductor.bsky.social, @jhsanchez.bsky.social, Mengyuan Shen, Jonathan Carroll and others in tidyomics for testing and getting this up and running
www.r-bloggers.com/2025/10/the-...
Thanks to @stemang.bsky.social, Maria Doyle @bioconductor.bsky.social, @jhsanchez.bsky.social, Mengyuan Shen, Jonathan Carroll and others in tidyomics for testing and getting this up and running
December 8, 2025 at 5:28 PM
tidyomics project 🔛 R-bloggers!
www.r-bloggers.com/2025/10/the-...
Thanks to @stemang.bsky.social, Maria Doyle @bioconductor.bsky.social, @jhsanchez.bsky.social, Mengyuan Shen, Jonathan Carroll and others in tidyomics for testing and getting this up and running
www.r-bloggers.com/2025/10/the-...
Thanks to @stemang.bsky.social, Maria Doyle @bioconductor.bsky.social, @jhsanchez.bsky.social, Mengyuan Shen, Jonathan Carroll and others in tidyomics for testing and getting this up and running
Our first Fall #tidyomics meeting will be this Wed 10 September, early in US / noon in Europe / late in Australia. Feel free to join if you're interested in what we are doing to make omics data more amenable to tidy data analysis.
Organized with Stefano @stemang.bsky.social
Organized with Stefano @stemang.bsky.social
September 8, 2025 at 7:45 PM
Our first Fall #tidyomics meeting will be this Wed 10 September, early in US / noon in Europe / late in Australia. Feel free to join if you're interested in what we are doing to make omics data more amenable to tidy data analysis.
Organized with Stefano @stemang.bsky.social
Organized with Stefano @stemang.bsky.social
June 25, 2025 at 2:46 PM
Excited to work with @stemang.bsky.social on tidyomics projects. Ad from Stefano:
"Postdoc and PhD positions available. Great scientific environment and great salary! You will also be exposed to and part of large-scale single-cell and spatial data analyses and AI for single-cell cancer immunology."
"Postdoc and PhD positions available. Great scientific environment and great salary! You will also be exposed to and part of large-scale single-cell and spatial data analyses and AI for single-cell cancer immunology."
Come and celebrate our 150th year. Explore our events, our history, and the foundation we’ve built for the future.
careers.adelaide.edu.au
June 21, 2024 at 4:30 AM
Excited to work with @stemang.bsky.social on tidyomics projects. Ad from Stefano:
"Postdoc and PhD positions available. Great scientific environment and great salary! You will also be exposed to and part of large-scale single-cell and spatial data analyses and AI for single-cell cancer immunology."
"Postdoc and PhD positions available. Great scientific environment and great salary! You will also be exposed to and part of large-scale single-cell and spatial data analyses and AI for single-cell cancer immunology."
Tidyomics, a collection of R packages that enable tidyverse-style syntax on biological datasets, is now published:
rdcu.be/dKNM6
Thanks to the hard work of the authors especially @stemang.bsky.social!
rdcu.be/dKNM6
Thanks to the hard work of the authors especially @stemang.bsky.social!
The tidyomics ecosystem: enhancing omic data analyses
Nature Methods - tidyomics offers a software ecosystem for omic data manipulation and analysis that bridges Bioconductor with the tidyverse framework.
rdcu.be
June 14, 2024 at 12:08 PM
Tidyomics, a collection of R packages that enable tidyverse-style syntax on biological datasets, is now published:
rdcu.be/dKNM6
Thanks to the hard work of the authors especially @stemang.bsky.social!
rdcu.be/dKNM6
Thanks to the hard work of the authors especially @stemang.bsky.social!
Stefano is an excellent workshop instructor!
Tidyomics is the application of tidyverse verbs directly to Bioconductor objects
Tidyomics is the application of tidyverse verbs directly to Bioconductor objects
I will be at the #ECCB2024 this September. If someone wants to join me in teaching/helping with the #tidyomics #workshop please let me know!
eccb2024.fi/workshops-tu... Together is more fun! :)
#Bioconductor #ECCB2024 #SAiGENCI #WEHI_research
eccb2024.fi/workshops-tu... Together is more fun! :)
#Bioconductor #ECCB2024 #SAiGENCI #WEHI_research
June 13, 2024 at 9:58 AM
Stefano is an excellent workshop instructor!
Tidyomics is the application of tidyverse verbs directly to Bioconductor objects
Tidyomics is the application of tidyverse verbs directly to Bioconductor objects
I love the idea of developing some code in plyranges / tidyomics format, figuring out what it is you want to compute (making some plots along the way), then hardening it into Rust with this library
I can imagine one day GPT with enough translated examples could even give you some starter code
I can imagine one day GPT with enough translated examples could even give you some starter code
May 28, 2024 at 8:20 PM
I love the idea of developing some code in plyranges / tidyomics format, figuring out what it is you want to compute (making some plots along the way), then hardening it into Rust with this library
I can imagine one day GPT with enough translated examples could even give you some starter code
I can imagine one day GPT with enough translated examples could even give you some starter code