scprocess is the result of an *unbelievable* amount of hard work by Maruša Koderman, PhD at University of Zürich co-supervised by me and @markrobinsonca.bsky.social. Maruša did so much: ideas, writing so much code, testing and debugging, writing all of the docs, tolerating me changing my mind... 🙈

😅 We are also excited to be presenting a Omnibenchmark workshop at ECCB in Geneva in Aug/Sept .. eccb2026.org/tutorials-wo...

So, this should be quite interesting! We just posted a BIG update to our Omnibenchmark "framework", basically a software layer to help you manage, build, standardize, and orchestrate reproducible and extensible (computational method) benchmarks .. (quite a mouthful) .. arxiv.org/abs/2409.17038

"Bulk RNA-seq to the rescue of differential expression analysis in single-cell transcriptomics" 🧫 📑 A new PCI Genomics recommendation by @mireyaplass.bsky.social: doi.org/10.24072/pci...

Orchestrating Spatial Transcriptomics Analysis with Bioconductor (including interoperability with Python) Paper: www.biorxiv.org/content/10.1... Book: bioconductor.org/books/OSTA/ #Rstats

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!

We are so excited to announce that our latest paper is out in @jem.org By combining single-cell RNA sequencing and 3D imaging, we reveal striking structural and molecular differences between human and mouse dermal lymphatic vasculature, opening up new perspectives on #Lymphatics and #HumanBiology

From @csoneson.bsky.social , @markrobinsonca.bsky.social & colleagues in @plos.org #Computational #Biology | Building a continuous #benchmarking ecosystem in #bioinformatics | #Education 🧬 🖥️ 🧪 🔓   ⬇️ journals.plos.org/ploscompbiol...

Hybrid untargeted and targeted RNA sequencing facilitates genotype-phenotype associations at single-cell resolution #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.1101/2025.11.06.686971v1

DESpace2: detection of differential spatial patterns in spatial omics data. #SpatialOmics #DifferentialSpatialPatterns #scRNAseq #Genomics #Bioinformatics @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1...

🧬 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

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...

Analysis of anatomical multi-cellular structures from spatial omics data using sosta https://www.biorxiv.org/content/10.1101/2025.10.13.682065v1

Looking for scientists working with long-read transcriptomics technologies to join a COST action proposal. Contact us!!! @nanoporetech.com @pacbio.bsky.social

Martin Emons on SpatialFDA - searching for differential colocalization in spatial omics data

EuroBioC2025 is in full swing here in Barcelona! Day 1 was full of great talks, conversations, and that amazing Bioconductor community energy. Excited for what’s ahead today and tomorrow! #EuroBioC2025 #Bioconductor #OpenScience #Community

We are excited to share the publication of our paper on exploratory spatial statistics for spatial omics data academic.oup.com/nar/article/...

MIMIC: a flexible pipeline to register and summarize IMC-MSI experiments https://www.biorxiv.org/content/10.1101/2025.07.08.663623v1

Update: We greatly revised our paper and renamed it “Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta”. We discuss the broad range of exploratory spatial statistics options for spatial Omics technologies and show relevant use cases. arxiv.org/abs/2412.01561

Did you ever notice discrepancies in benchmarking of bioinformatics tools? We did too! Setting out to benchmark spatial clustering methods, we encountered major reproducibility issues in previous benchmarks and questionable "ground truths". More in our preprint: www.biorxiv.org/content/10.1...

DESpace2: detection of differential spatial patterns in spatial omics data https://www.biorxiv.org/content/10.1101/2025.06.30.662268v1

A Systematic Benchmark of High-Accuracy PacBio Long-Read RNA Sequencing for Transcript-Level Quantification. #HiFi #LongReads #Sequencing #Transcriptomics @pacbio.bsky.social @biorxivpreprint.bsky.social www.biorxiv.org/content/10.1...

🤖 SIB supplies the foundation of transformational AI by providing: ⭐ gold-standard training data through curated databases 🔗 connected information through knowledge representation 💪 trustworthy evaluation through benchmarking. See how in the #SIBProfile 2025: issuu.com/sibswissinst...

Pseudobulk DGE #RStats journal club * #muscat doi.org/10.1038/s414... @helucro.bsky.social * pbDD doi.org/10.1101/2023... @davi1893.bsky.social * #dreamlet doi.org/10.1101/2023... ‪@panosroussos.bsky.social * #distinct doi.org/10.1214/22-A... @markrobinsonca.bsky.social youtu.be/TB9dfKPfns8

Heads-up that Genome Biology is starting a new benchmark collection ("Benchmarks v2.0"): www.biomedcentral.com/collections/...

Honored to deliver the opening keynote talk at the Modern Benchmarking Conferene in Ascona a very much needed meeting organizad by @markrobinsonca.bsky.social @iscb.bsky.social sites.google.com/view/ascona2...

From @csoneson.bsky.social , @mramos148.bsky.social, @jorainer.bsky.social & colleagues in @plos.org #Computational #Biology | Eleven quick tips for writing a #Bioconductor package | #Bioinformatics #Education #Rstats #PLOSCBQT 🧬 🖥️ 🧪 🔓 ⬇️ journals.plos.org/ploscompbiol...

Quick update. We have a pretty exciting lineup of topics/speakers in and around benchmarking that will be presented in Ascona at the end of the month: sites.google.com/view/ascona2... There are few registration slots left, so if you are interested to join us, get in touch.

Do you want to learn more about the statistical analysis of proteomics, metabolomics, single-cell and spatial transcriptomics? Do you want to up your game with R and Bioconductor? All of this while enjoying summer in the beautiful Italian Alps? Join us for the 21st edition of CSAMA July 6-11!

Another preprint from our group this week .. see @siyuanluo.bsky.social's explainer below ..

edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets. #EdgeR #DifferentialAnalysis #Bioinformatics #Genomics @biorxivpreprint.bsky.social 🧬 🖥️ www.biorxiv.org/content/10.1...

A little piece that's been in the works with former MSc, now PhD student, Jiayi Wang & @markrobinsonca.bsky.social in the multi-sample/-condition/-subpopulation theme: ...

Another fresh preprint from our group about spatial statistics for spatial omics data .. @samuelgunz.bsky.social gives a nice explainer below.

Interested in spatial statistics for spatial omics data? Check out our new resource: pasta. We show how different technologies lead to different data modalities give and overview of point-pattern and lattice-based spatial analysis. Feedback welcome! arxiv.org/abs/2412.01561

Thread below from @helucro.bsky.social on a new preprint from us .. trying to separate "type" from "state" genes at the feature selection step ..

2. The reviewer culture makes it difficult to get funding for proposals that are genuinely high risk: where little of the work has been done in advance. But also proposals that are meaningfully low risk: the benchmarking and maintenance of important tools.

so one last call .. abstracts due today (6pm, time zone of your choice 😀) .. Ascona, Switzerland in March 2025 .. conference about all things benchmarking: sites.google.com/view/ascona2... Abstract submission link: t.co/zGGZ9Xd60E

Deadline for abstracts for this exciting meeting on benchmarking in computational biology is this Monday @markrobinsonca.bsky.social @SIB.mstdn.science.ap.brid.gy sites.google.com/view/ascona2... #bioinformatics #ComputationalBiology