iiinova — where your digital self keeps evolving

Reposted by Juan Henao

BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 10/07/2026

"Maintaining and refining the Tidyomics ecosystem: enhancing core packages and interoperability for EuroBioc2026" 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]

Figure 1: Schematic representation of the Tidyomics hackathon aims. 1. We introduced tidyAnnData to provide tidy operators for AnnData objects; 2. We fixed major bugs in information accessibility for Tidyomics core packages; 3. We updated and extended Tidyomics packages such as DFplyr and tidybulk; 4. We provide a comprehensive and concise vignette for the tidySingleCellExperiment package. This plot was created by Google Nano Banana 2.

001

Reposted by Juan Henao

Wolfgang Huber @wkhuber.bsky.social · 16/06/2026

Many results, new or improved packages, and future directions in this report on the Bioconductor Spatial Data and Image Analysis Hackathon that took place in Venice in April 2026. osf.io/preprints/bi...

Participants of the Bioconductor Spatial Data and Image Analysis Hackathon in Venice, April 2026.

Participants of the Bioconductor Spatial Data and Image Analysis Hackathon in Venice, San Servolo, April 2026.

0212

Reposted by Juan Henao

BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 15/06/2026

"Bioconductor Spatial Data and Image Analysis Hackathon" doi.org/10.37044/osf.io/9ej32_v1 "We report the outcomes of the Bioconductor Spatial Data and Image Analysis Hackathon, held in Venice, Italy in April 2026. Twenty-seven researchers and […] [Original post on fediscience.org]

One of the figures from the preprint. It shows a 2d image of tissue, colored with a red stain, showing the red and white image that we see. At the top there is the text "Overlay: Terra Image and Segmentation".

076

Reposted by Juan Henao

Bioconductor @bioconductor.bsky.social · 31/05/2026

Great to see a #EuroBioC2026 hackathon project sharing plans 👏 Tidyomics team outline what participants can get involved in.

042

Reposted by Juan Henao

Stefano Mangiola @stemang.bsky.social · 30/05/2026

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

EuroBioC2026 Tidyomics Hackathon – tidyomicsBlog

An invitation to join the Tidyomics community hackathon at EuroBioC2026 in Turku, Finland.

083

Reposted by Juan Henao

Gregor Sturm @grst.bsky.social · 29/05/2026

Happy to announce the release of IggyTop, a metadatabase for immune receptor–epitope interactions. It's integrated with scirpy v0.24 so you can readily use it to annotate your single-cell TCR datasets. iggytop.readthedocs.io/en/latest/

198

Reposted by Juan Henao

Stefano Mangiola @stemang.bsky.social · 08/05/2026

New #tidyomics blog post! 🎉 #tidySummarizedExperiment greatly simplifies your omics workflows, giving tidyverse capabilities. We have improved its performance 30x on large datasets with tens of thousands of samples! tidyomics.github.io/tidyomicsBlo... Plz share! @mpibiochem.bsky.social

tidyomics.github.io

Speeding up tidySummarizedExperiment through query optimisation and the plyxp backend – tidyomicsBlog

Performance optimisation of tidySummarizedExperiment and related benchmark.

0135

Juan Henao @jhsanchez.bsky.social · 24/04/2026

HCA has transformed single-cell biology, but lacks standardized QC, normalization, annotation, aggregation, and cell-cell communication layers. Here, Mengyuan Shen, led by @stemang.bsky.social, developed #cellNexus: www.biorxiv.org/content/10.6... PyPi (my contribution): pypi.org/project/cell...

biorxiv.org

000

Reposted by Juan Henao

Stefano Mangiola @stemang.bsky.social · 24/04/2026

#cellNexus is out! -> "Quality control, annotation, aggregation and analytical layers for the Human Cell Atlas data" - QC layers - Consensus cell annotation layers - Pseudobulk aggregation of the whole human atlas - R/Python APIs cellNexus.org Preprint: www.biorxiv.org/content/10.6...

32210

Reposted by Juan Henao

Stefano Mangiola @stemang.bsky.social · 06/01/2026

Reproducibility is key to science. In computational biology, we routinely manipulate high-dimensional data (spatial, single-cell, bulk) through filtering, normalisation and transformation. Capturing those steps clearly improves reproducibility and transparency. tidyomics.github.io/tidyomicsBlo...

tidyomics.github.io

Omicslog – tidyomicsBlog

Providing logging capabilities for SummarizedExperiment objects.

1218

Reposted by Juan Henao

Stefano Mangiola @stemang.bsky.social · 18/12/2025

A great last #tidyomics meeting of the year, looking forward to more of these in 2026! @bioconductor.bsky.social

021

Reposted by Juan Henao

Stefano Mangiola @stemang.bsky.social · 15/12/2025

The last #tidyomics meeting of the year is in 2 days. Everyone welcome! - 16 Dec, 3:30 pm (EST; New York) - 16 Dec, 9:30 pm (CET; Berlin) - 17 Dec, 7:30 am (AEDT; Melbourne) We will chat about plans for next year. Zoom link: shorturl.at/Epbbc @mikelove.bsky.social @bioconductor.bsky.social

052

Reposted by Juan Henao

Stefano Mangiola @stemang.bsky.social · 07/12/2025

It's official! The #tidyomics blog is up! 🚀 Here, the introductory post tidyomics.github.io/tidyomicsBlo... This blog aims to publish not only news about our community but also anything related to tidy interfaces, opinions, events, and more. Plz share! 🙏 @bioconductor.bsky.social #rstats

tidyomics.github.io

The Tidyomics Ecosystem – tidyomicsBlog

An introduction to the tidyomics ecosystem, including principles, core packages, publications, and community resources for tidy omic analysis.

02713

Reposted by Juan Henao

Michael Love @mikelove.bsky.social · 08/09/2025

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

1144

Reposted by Juan Henao

Stefano Mangiola @stemang.bsky.social · 27/03/2025

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

012