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Stefano Mangiola @stemang.bsky.social · Sep 8

Join us for another tidyomics meeting tomorrow!

We will chat about several news
- tidyprint
- tidybulk V2
- omicslog
- and more!

Michael Love @mikelove.bsky.social · Sep 8

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

Meeting agenda

Sep 10, 2025
Attendees:
Links:
Agenda (feel free to add your items):
• Blog almost ready for R blogger linkage thanks to @Izabela Mamede, @Mengyuan Shen and @Maria Doyle
• New posts from many including
@Juan Henao and myself
• Ideas for other posts?
• There is tidybulk v2 ready to be submitted. Some feedback would be nice there.
• Stefano's new speedy code in tidySE
• https://github.com/tidyomics/
genomics-todos/issues/19#is suecomment-3239791713
• https://github.com/tidyomics/t
idySummarizedExperiment/i ssues/106
• Report back from tidyomics workshop at useR! (Justin and Mike)
• Other projects in the works?
• Ideas for engaging new users?
New developers?

These are the corresponding times for your meeting:
Location
Local Time
Durham (USA - North Carolina)
Wednesday, September 10, 2025 at 6:00:00 am
Adelaide (Australia - South Australia)
Wednesday, September 10, 2025 at 7:30:00 pm
Paris (France - Paris) |
Wednesday, September 10, 2025 at 12:00:00 noon
Corresponding UTC (GMT)
Wednesday, September 10, 2025 at 10:00:00

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Stefano Mangiola @stemang.bsky.social · Aug 26

Join us for an interesting discussion on using AI with foundational models in biology!

Australian BioCommons @ausbiocommons.bsky.social · Aug 12

Next in our #AI webinars:

Stefano Mangiola @saigenci.bsky.social
talks AI models in #SingleCell and if they can uncover biological patterns

Anh TN Nguyen @monashuniversity.bsky.social shares how deep learning is accelerating #DrugDiscovery for GPCRs

More info www.biocommons.org.au/events/ai-se...

Flyer advertising upcoming webinars. Photos of the speakers are shown on the right.

The words read: Dr Stefano Mangiola (SAiGENCI)
“Improving the interpretability of AI models for cell biology and precision medicine”

Dr Anh TN Nguyen (Monash)
“Bridging pharmacology and AI: Accelerating GPCR drug discovery with deep learning”

26 August 2025
12 - 1 pm AEST

Stefano Mangiola @stemang.bsky.social · Aug 6

Join #AI and #Immunology!

📢 Fully funded #PhD @saigenci.bsky.social: develop AI to chart immune diversity across the population, in #cancer.

CV, transcript, and a one-page statement by 30 August 2025 → www.linkedin.com/feed/update/...

#PhDOpportunity #MachineLearning #SingleCell

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Stefano Mangiola @stemang.bsky.social · Jul 30

Two days to apply for a BiocAsia workshop!

- Did you develop a package you want to showcase?
- You want to share an analysis workflow for your favourite data type?

This is your time to share this with the community!

Submission -> biocasia2025.bioconductor.org

@bioconductor.bsky.social

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Stefano Mangiola @stemang.bsky.social · Jul 14

BiocAsia will collaborate with ABACBS for the 2025 conference (Adelaide) to bring you a full day of workshops!

Have you thought about teaching a workshop about your or someone else's package or a workflow?

This is the time! Submit your proposal by the 1st of August.

Bioconductor @bioconductor.bsky.social · Jul 11

📣 BioCAsia 2025: Call for Workshops

Join the Bioconductor stream at ABACBS 2025 in Adelaide!

Submit your hands-on workshop EOI by August 1.

Flexible 90-min blocks.

➡️ www.abacbs.org/abacbs-2025-...

#Bioconductor #BioCAsia2025 #RStats

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Reposted by Stefano Mangiola

Bioconductor @bioconductor.bsky.social · Jul 1

Big thanks to everyone who made #GBCC2025 a fantastic week of science, collaboration, and community!

Highlights for Bioconductor included keynotes, hands-on projects, and great conversations 💻🧬

@galaxyproject.bsky.social @bioconductor.bsky.social

Vince Carey opening GBCC2025 with a slide highlighting Bioconductor’s technical and community advances.

Charlotte Soneson delivering her keynote titled “From classes to community: how Bioconductor has advanced my research.”

Slide showing GBCC2025 sponsors and supporters - CZI, Limagrain, GalaxyWorks, Bristol Myers Squibb, R Consortium, Gigascience, ELIXIR, NHGRI

Large group photo of GBCC2025 attendees outdoors at Cold Spring Harbor Laboratory, smiling and gathered on the steps.

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Stefano Mangiola @stemang.bsky.social · Jul 2

What a cover! Looking forward to sharing our work with you!

Doppeldata - Adelaide Bioinformatics @doppeldata.au · Jul 1

Seminar this Friday July 4th 1.00pm: “Modelling and Democratising the Human Cell Atlas” with @stemang.bsky.social, Haroon Shakeel & Chen Zhan (@saigenci.bsky.social)

Details & zoom info: doppeldata.au/events/event...

#Bioinformatics #SingleCell #HumanCellAtlas #Adelaide #Genomics

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Stefano Mangiola @stemang.bsky.social · May 23

Today, I had a blast at the @mig-unimelb.bsky.social
MIG symposium, showcasing our use of mixed linear models at scale and #AI tools to study #singlecell cancer immunology.

Thanks Heejung, Kim-Anh and all the MIG!

events.unimelb.edu.au/MIG/event/45...

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Stefano Mangiola @stemang.bsky.social · May 23

Thanks @physaliacourses.bsky.social, it was a blast! And the great active audience made it so enjoyable!

Physalia-courses@Online @physaliacourses.bsky.social · May 21

🚀 We’re wrapping up our 3-day Spatial Omics in R/ @bioconductor.bsky.social workshop!

A huge THANK YOU to @stemang.bsky.social Malvika and all our attendees who made this event a success 🎉

Until next time — www.physalia-courses.org/courses-work... 🧬🗺️
#SpatialOmics #Bioconductor #RStat

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Stefano Mangiola @stemang.bsky.social · May 19

Amazing crew! Tomorrow, we will show the Physalia crew how to use #tidyomics to manipulate and analyse spatial data!

Physalia-courses@Online @physaliacourses.bsky.social · May 19

🚀 Just kicked off our Spatial Omics in R/Bioconductor course with @stemang.bsky.social
In this 3-day course, we're gonna explore spatial technologies & hands-on data analysis in R and Bioconductor using tidy principles🧬🧠📊
www.physalia-courses.org/courses-work...
#SpatialOmics #RStats #Bioconductor

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Stefano Mangiola @stemang.bsky.social · Mar 27

In few hours we have the second #tidyomics meeting! where we will talk about workshops, communication and education and more.

Thursday March 27 with a Europe friendly meeting time (12:00 CET)

Join the @bioconductor.bsky.social slack channel to know more #tidiness_in_bioc channel

Join us

Stefano Mangiola @stemang.bsky.social · Mar 17

Great first #tidyomics meeting, covering 3 continents! 🌍

We discussed data representation with #tidyprint. Stay tuned for the next one to discuss workshop delivery, education and more!

Join the slack channel #tidiness_in_bioc community-bioc.slack.com/archives/CEQ...

@bioconductor.bsky.social

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Stefano Mangiola @stemang.bsky.social · Mar 17

We encourage diverse participation regardless of background, gender, or beliefs.

The meetings are friendly and open!

You don't need to participate actively; you can join simply to stay updated on #tidyomics development.

We welcome you!

Stefano Mangiola @stemang.bsky.social · Mar 17

Great first #tidyomics meeting, covering 3 continents! 🌍

We discussed data representation with #tidyprint. Stay tuned for the next one to discuss workshop delivery, education and more!

Join the slack channel #tidiness_in_bioc community-bioc.slack.com/archives/CEQ...

@bioconductor.bsky.social

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Reposted by Stefano Mangiola

Physalia-courses@Online @physaliacourses.bsky.social · Mar 14

🚀 Interested Spatial Omics with R/Bioconductor?
🧨Do you want to learn how to analyse these data in R with the #tidyverse?

Join us in May for this course with @stemang.bsky.social & @lgmartelotto.bsky.social

🔗 www.physalia-courses.org/courses-work...

#SpatialOmics #Bioinformatics #RStats

spatial Omics in R/Bioconductor

19-21 May 2025 To foster international participation, this course will be held online

www.physalia-courses.org

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Stefano Mangiola @stemang.bsky.social · Mar 11

True 5PM. Sorry for that.

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Stefano Mangiola @stemang.bsky.social · Mar 11

@bioconductor.bsky.social @mikelove.bsky.social

1

Stefano Mangiola @stemang.bsky.social · Mar 11

Tomorrow, we will have our first #tidyomics meeting for 2025! We will discuss how to centralise tidy display for biological data -> github.com/tidyomics/ti...

Wednesday 12th of March
- 4PM NY
- 9PM London
- 8AM (Thursday) Melbourne

details -> community-bioc.slack.com/archives/CEQ...

Pls share!

GitHub - tidyomics/tidyprint

Contribute to tidyomics/tidyprint development by creating an account on GitHub.

github.com

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Reposted by Stefano Mangiola

Bioconductor @bioconductor.bsky.social · Mar 4

📅 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

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

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Stefano Mangiola @stemang.bsky.social · Feb 11

📢 An exciting #Postdoc position opened in our laboratory for a junior #Bioinformatician!

Developing #Bioinformatic and #AI tools to advance precision oncology using the available #singlecell / #spatial data universe.

careers.adelaide.edu.au/cw/en/job/51...

Pls share! 🙏

#postdocposition

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Stefano Mangiola @stemang.bsky.social · Jan 29

@bhuvad.bsky.social

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Stefano Mangiola @stemang.bsky.social · Jan 22

The Python implementation is in Beta, and we welcome feedback!

Stefano Mangiola @stemang.bsky.social · Jan 22

We (Chen Zhan!) just launched #sccomp for #Python!

Testing for differences in cell-type proportion in #singlecell #spatial data?

#sccomp is a mixed-effect Bayesian model
- Use sum-constrained BetaBinomial distribution
- Outliers detect.
- Remove unwanted effects

github.com/MangiolaLabo...

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Stefano Mangiola @stemang.bsky.social · Jan 20

A great Team!

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Stefano Mangiola @stemang.bsky.social · Jan 8

The hope is that this collaborative model can be applied more broadly, creating a virtuous circle to boost research and support research diversity.

Contributions are welcome from diverse computational fields, e.g. #Physics #ecology #maths #biology, ...

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Stefano Mangiola @stemang.bsky.social · Jan 8

Would you open your paper to a modular open-collaboration model?

It was game-changing for #tidyomics

If you love #crowdResearch and #CommunityBuilding have your say on the #crowdToPaper model guidelines

Comment on the shared doc: docs.google.com/document/d/1...

Please share 🙏

CTP-1.0

CTP guidelines 1.0 Definition and Operational Details of the Crowd-to-Paper Model This document, called “CTP-1.0”, is a template that includes the guiding principles of projects based on the crowd-to-...

docs.google.com

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