Marco Varrone

Excited that our paper "CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity" is finally out! 🎉 A spatial clustering method for any type of spatial proteomics, transcriptomics, or even epigenomics data! nature.com/articles/s4158…

@kenbwork @illumina @10xGenomics Thank you very much! Maybe I am missing something but if it was sterics/geometry, how would thousands of copies be able to fit inside a well?

@MarcoVarrone @illumina @10xGenomics Awesome piece. I'm not sure this is technically correct: "The replication happens so fast that there is not time for another molecule to enter the well, so every well contains copies of only one molecule." My understanding this is more chemistry and sterics/geometry than speed

I collected all of what I could find about the upcoming @illumina Spatial Transcriptomics technology, with some predictions about costs and sensitivity compared to @10xGenomics Visium HD. batcheffect.com/p/the-giant-wa…

Lastly, big thanks to @LukasHats for spotting a memory leak in the differential neighborhood enrichment function! This pushed me to refactor it completely. Now it's much faster and more memory-efficient. 🚀 5/5

Key takeaway for choosing a dependency to add to your library. Choose either: 1️⃣ Well-maintained packages (e.g., PyTorch, Scanpy, Seurat). 2️⃣ Simple packages that don't require updates (e.g., tqdm). 3️⃣ Packages you are ready to take over if the original maintenance stops 4/5

🎉 We released CellCharter v0.3.2! - Now part of the @scverse_team ecosystem - More efficient differential neighborhood enrichment - Peak finding for cluster stability - Compatible with the latest PyTorch A few lessons learned along the way 🧵 1/5 github.com/CSOgroup/cellc…

New Batch Effect blog post! 🧬 Finding domains from spatial omics data has exploded in popularity, with over 87 methods! However, two mistakes in their evaluation might be leading us in the wrong direction. batcheffect.com/p/the-pitfalls…

@ItaiYanai That's why every scientist should have a blog for explaining the thought process without going through another round of reviews

Is the scientific paper a fraud? Peter Medawar (Nobel Prize winner) suggested that publications are overly structured and formal, giving only a sanitized version of the discovery without revealing the thought process that actually led to it.

Call for PhD in quantitative Biology!! Applications open ... unil.ch/quantitative-b… #PhD #computationbiology #quantititivebiology

The main lesson is whenever you start a new project, start simple, then build up from there. 📈 Sometimes, that’s all it takes.

Neighborhood aggregation proved remarkably effective in capturing crucial spatial relationships while being scalable to millions of cells. It is also the base of CellCharter, the framework we developed during my PhD to study domains from spatial omics data.

New Batch Effect blog post! We often think complex algorithms are the key to analyzing spatial omics data. But sometimes, simplicity can be as effective. 🧵 batcheffect.com/p/when-simple-…

@mo_lotfollahi Thanks Mo!

@MarcoVarrone Cool stuff Marco, super informative

New blog post! We are used to thinking that, when an organism has cancer, all other cells will fight it. We are now realizing that this is not true, and some of these cells may even help it. In this latest Batch Effect post I talk about 4 aspects 🧵 batcheffect.com/p/the-hidden-a…

After a few immunology-focused posts, in the next Batch Effect posts we will shift to more computational gears and see how to actually find cell communities from spatial omics data. Stay tuned!

3. How spatial omics can identify cell communities and true cell interactions to understand what is really happening. 4. How discoveries driven by spatial omics will lead to new effective therapies.

Earlier this week we carried out a preliminary analysis of our first @10xGenomics Xenium prime (5,000 gene) run. We had designed this experiment to get a sense of how the prime chemistry performed compared to the Xenium V1 chemistry.