Extremely proud of @justjhong.bsky.social @khushipde.bsky.social for bringing this innovation to life! #AMICI🤝 redefines #attention for cell–cell interaction inference from #spatial #transcriptomics going beyond proximity to capture who talks to whom, at what distance and w/ what downstream impact!

Khushi Desai@khushipde.bsky.social · 11mo ago

1/ I’m excited to share recent work on inferring cell-cell interactions using attention by @justjhong.bsky.social and me, supervised by @elhamazizi.bsky.social . Open the thread 🧵 for a brief overview of our method. bioRxiv link: www.biorxiv.org/content/10.1....

It's taken more than 2 years but we can officially announce anndataR! There's still a lot of features to add but we hope a robust, "official", R-native H5AD reader/writer will unlock the defacto single-cell storage format for R users by avoiding issues with current solutions like zellkonverter.

Louise Deconinck@louisedck.bsky.social · 12mo ago

We're excited to share that our preprint on anndataR, a new package bringing Python's AnnData to R, is now available on bioRxiv 🎉 🔗 Read the paper: www.biorxiv.org/content/10.1... 💻 Check the package in action: anndatar.data-intuitive.com

scverse turns 3! What started as a shared vision for interoperable single-cell analysis has become a vibrant, global community. From AnnData to full multimodal pipelines, we’re building the future of everything single-cell and spatial omics, together. Here’s to what’s next!

We identify evidence of off-target probe binding in the 10x Genomics #Xenium v1 Human Breast Gene Expression Panel, compromising the accuracy of resulting #singlecell #spatialtranscriptomics profiles See our preprint for more details: www.biorxiv.org/content/10.1... #AcademicSky 🧵👇 1/n

Evidence of off-target probe binding in the 10x Genomics Xenium v1 Human Breast Gene Expression Panel compromises accuracy of spatial transcriptomic profiling

The accuracy of spatial gene expression profiles generated by probe-based in situ spatially-resolved transcriptomic technologies depends on the specificity with which probes bind to their intended tar...

biorxiv.org

A pre-trained SCVI model of our Tahoe-100M cell atlas is now available as a HubModel! It can be used for gene expression visualization, differential expression, or cell clustering. Available at Hugging Face with instructions on how to load it (see thread)

I am Stoked about our upcoming @scverse.bsky.social and @owkin.bsky.social hackathon, focused on spatial omics data analysis. 📅 March 17-19, 2025 📍 Owkin office, Paris Apply now: docs.google.com/forms/d/e/1F...

Scverse x Owkin Hackathon in Paris

We're pleased to announce the next Scverse Hackathon will take place in the Owkin offices in Paris from 17/03/2025 9am to 19/03/2025 1:30pm. This hackathon is a joint initiative between the scverse c...

docs.google.com

I was just looking at our @scverse.bsky.social zulip chat statistics and am super happy about our steady and healthy growth. The two bursts are our official launch in May 2022 and the inaugural scverse conference in September of 2024. Please join us! scverse.zulipchat.com

Wanted to learn more about VisiumHD barcodes to help build better tools for processing that exciting data I asked 10x about parsing the binary spatial information file, they said: "...the Visium HD barcodes...are proprietary..." C'mon 10x. You're shooting yourselves (and users) in the foot here!

Explore the scverse Starter Pack! Stay informed about the latest scverse events, software updates, and community news. Everything you need to know about foundational tools for single-cell omics analysis in one place. go.bsky.app/UvFMa8d