Helena Lucia Crowell

Standing on the shoulders of giants: immense thanks also to @bioconductor.bsky.social core, its community and developers, for the two decades of foundational work we could build on today.

Shout out and thanks to everyone who was a part of this; one couldn’t have done it alone.

@rgottardo.bsky.social
@markrobinsonca.bsky.social
@stephaniehicks.bsky.social
@lmweber.bsky.social
and many more.

Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA.

Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).

It’s been a joy working with you @estellayixingdong.bsky.social!

Bioconductor Seminar Series flyer. Title: “Deep-learning-based Gene Perturbation Effect Prediction Does Not Yet Outperform Simple Linear Baselines.” Event on Dec 2, 2025 at 9 PM CET / 3 PM EST / 12 PM PST. Speakers: Constantin Ahlmann-Eltze, Wolfgang Huber, Simon Anders. Discussant: Davide Risso. Includes a “Register for Zoom Link” button, QR code, and Bioconductor logo.

📣 Calling Bioconductor users and developers! 🧬 ✨

Join our new quarterly online seminar series featuring contributor innovations and discussions on package integration. Enjoy 30 minutes of insights, 15 minutes of guided discussion, and 15 minutes of open Q&A. Share questions live or in chat!

[source: Nature Genetics]

🫠

Bioconductor - Bioconductor 3.22 Released 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…

🚀 Bioconductor 3.22 is released!

Thanks to all developers and community members for contributing to the project!

🔗 Please see the full release announcement here: bioconductor.org/news/bioc_3_...

🧬 EuroBioC2026 is coming to Turku, Finland, from June 3–5, 2026!

Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.

👉 More details soon at eurobioc2026.bioconductor.org

EuroBioC2025 conference recap – Bioconductor community blog Highlights from the 2025 European Bioconductor Conference in Barcelona

Thank you to all our amazing sponsors, organizers, speakers, and attendees for making #EuroBioC2025 in Barcelona such a success!

Read the full recap blog post here👉 blog.bioconductor.org/posts/2025-1...

And, see you next year at #EuroBioC2026! 🎉

#Bioconductor #Community #Conference

I'm very excited to share our latest preprint!

We introduce structure-based analysis of spatial omics data – an approach that focuses on multi-cellular anatomical structures rather than single cells.

We also present sosta to facilitate this type of analysis: bioconductor.org/packages/sos...

It’s happening 🤗
#EuroBioC2025
@bioconductor.bsky.social

A transcriptional map of human tonsil architecture: beyond the sum of (single cell) parts The tonsil is a highly compartmentalized organ in which different microanatomical structures orchestrate designated (immune) functions. We use this already well-studied tissue to survey spatial molecu...

🚀 Spatial Transcriptomics (Imaging) + Spatial-centric analyses by @helucro.bsky.social : the way to truly interrogate tissues!!!
📖 Read our pre-print on human tonsil architecture (full of tonsiLove ♥️) here: doi.org/10.1101/2025...

Harnessing the potential of spatial statistics for spatial omics data with pasta Abstract. Spatial omics allow for the molecular characterization of cells in their spatial context. Notably, the two main technological streams, imaging-ba

We are excited to share the publication of our paper on exploratory spatial statistics for spatial omics data

academic.oup.com/nar/article/...

Bioconductor nominations graphic with CAB and TAB illustrations and www.bioconductor.org

🌟 One Week Left to Nominate for Bioconductor’s 2025 Advisory Boards! 🌟

Help shape the future of open science and bioinformatics by joining the Community or Technical Advisory Board.

🗓️ Deadline: August 31
📥 Apply or nominate:
CAB 👉 forms.gle/8NYxRGhprfuN...
TAB 👉 forms.gle/eqef9ThpUypc...

Ukrainian Biological Data Science Summer School 2025 – Huber Group @ EMBL Uzhhorod, 19 July - 1 August 2025: the third edition

In July we had the 3rd edition of the Ukrainian Biological Data Science Summer School.
Now a regular, it has created a sense of community: young people eager to learn new topics, network across the country&world. Seeing how science is a positive&optimistic force.

www.huber.embl.de/group/posts/...

European Bioconductor Conference 2025 – EuroBioC2025 The European Bioconductor Conference (EuroBioC2025) will take place on September 17th to 19th, 2025, in Barcelona, Spain. EuroBioC2025 will bring together the Bioconductor community to showcase the…

⏳ One week left to register!
Join us at EuroBioC2025 in Barcelona and the Bioconductor Carpentry Workshops for hands-on learning, community building, and cutting-edge bioinformatics.

🗓️ Registration closes August 28 — don’t miss out!
🔗 eurobioc2025.bioconductor.org

#EuroBioC2025 #RStats

Bioconductor nominations graphic with CAB and TAB illustrations and www.bioconductor.org

🌟 Bioconductor 2025 CAB & TAB nominations are open!

Join our advisory boards to support community growth or guide technical strategy.

📅 Apply by Aug 31
CAB: forms.gle/8NYxRGhprfuN...
TAB: forms.gle/eqef9ThpUypc...

#Bioconductor #RStats

A musical note composed of small hexagonal package stickers, arranged in a gradient from dark to vibrant colors. The overall shape resembles a quaver (eighth note), forming a colorful, pixelated mosaic.

🎨 Calling all Bioconductor package developers!

We’re building a Sticker Hexwall for #EuroBioC2025

Submit your package sticker by July 22 to be featured:
🔗 eurobioc2025.bioconductor.org/pages/hexwal...

Know a package that’s missing a sticker? Encourage them to join in!

#Bioconductor #RStats

Did you know you can infer CNVs using image-based spatial transcriptomics?

Check it out in our latest preprint.

Bioconductor and ggplot2 4.0.0: What’s Changing and How to Prepare – Bioconductor community blog Preparing for the upcoming update - key changes, potential breakages, and what developers and users can do

📝 New blog post: Bioconductor and ggplot2 4.0.0 - What’s Changing and How to Prepare

A major ggplot2 update is coming and may impact Bioconductor packages. What’s changing, how to test, and where to get help 👉 blog.bioconductor.org/posts/2025-0...

#Bioconductor #RStats

In Situ Inference of Copy Number Variations in Image-Based Spatial Transcriptomics https://www.biorxiv.org/content/10.1101/2025.07.02.662761v1

PS: Main figs are only a (thoughtful) selection. There’s so much more (pretty) data, partly in the supp. — worth checking out!

PPS: all data/results are up for grabs, including R-, Py-friendly & language-agnostic versions. — developers, go!

- we observe a bifurcating tumor evolution: concordant with malignancy assessments; one end-point organizes into concentric layers & maps to invasion/metastatic sites

- we introduce “transition crypts” — split histological & transcriptional makeup (from crypt fusion or abrupt transformation?)

- sections that span reference, pre- & malignant regions let us look into what happens along the molecular/spatial neoplastic transformation axis (compositional drifts, cellular density & heterogeneity, pathways & signaling, etc.), from cells/crypts via niches to tissue-wide scale

Thx @hoheyn.bsky.social & Sabine Tejpar for getting/keeping the game afoot;
KU Leuven & @brukerspatial.bsky.social teams for your support.

These data were no breeze yet real gratifying; in brief:

- we survey 3.5M cells (1.6k FOVs = 4.3cm2) via WTx CosMx SMI & snPATHO-seq + digital histopatholgy

Special thx @pascual-reguant.bsky.social & Irene Ruano for your rare combi of standards, humanity, passion & perseverance. It wasn't always fun'n'giggles, but I laughed & learned so much from/with you (e.g., how to say & spell “tubulovillous”). Muchísimas gracias para todo mis ángeles.

Tracing colorectal malignancy transformation from cell to tissue scale The transformation of normal intestinal epithelium into colorectal cancer (CRC) involves coordinated changes across molecular, cellular, and architectural scales; yet, how these layers integrate remai...

Going from methods dev to full on cancer bio has been tough. All the more excited to see this out at last—

www.biorxiv.org/content/10.1...

@pascual-reguant.bsky.social
@brukerspatial.bsky.social
@hoheyn.bsky.social

EuroBioC2025 late-breaking poster abstract submission Please fill the form below before the end of Friday July 11th, 2025, to submit an abstract for a poster to be considered for presentation at EuroBioC2025 in Barcelona on September 17-19, 2025…

📣 Late-breaking poster call for #EuroBioC2025 is now open!

Submit by July 11 to present your work in Barcelona this September.
🔗 forms.gle/ewTGdKzB2xyE...
📅 Notifications by July 15

#Bioconductor #Bioinformatics

Ask and you shall receive – Bioconductor community blog Discussion of evolving complexity and value of the Bioconductor ecosystem.

📝 New Bioconductor Blog Post!
We’ve just launched the first in a new series by Vince Carey, founding contributor to Bioconductor and core developer, exploring the evolving complexity and value of the Bioconductor ecosystem.
Check it out 👉 blog.bioconductor.org/posts/2025-0...
#Bioconductor #RStats

EuroBioC goes south! The most south since… ever? Come join us in Barcelona 🇪🇸 for great science, community, and scholarly chats by the sea 🌊