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Estella Yixing Dong

@estellayixingdong.bsky.social

Applied Machine Learning @Bayer | PhD @CHUVLausanne | Immunotherapy, Single-Cell RNAseq, Spatial Transcriptomics, Statistics and Machine Learning. 📷⛸️🏔️

Posts Replies Media

Reposted by Estella Yixing Dong

Lukas Weber @lmweber.bsky.social · 22/11/2025

This was a huge effort by many contributors, in particular @helucro.bsky.social @estellayixingdong.bsky.social @rgottardo.bsky.social @markrobinsonca.bsky.social @stephaniehicks.bsky.social , and the @bioconductor.bsky.social core team and community. Thank you everyone! 🎉

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Reposted by Estella Yixing Dong

Helena Lucia Crowell @helucro.bsky.social · 21/11/2025

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.org

Orchestrating Spatial Transcriptomics Analysis with Bioconductor

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Reposted by Estella Yixing Dong

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 21/11/2025

Orchestrating Spatial Transcriptomics Analysis with Bioconductor www.biorxiv.org/content/10.1101/202…

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Reposted by Estella Yixing Dong

Raphael Gottardo @rgottardo.bsky.social · 22/06/2025

🎉 New paper alert. We benchmarked Visium, GeoMx, and Chromium for FFPE tumor analysis. Thanks @estellayixingdong.bsky.social for pushing this forward, & MOSAIC collaborators! 📄 www.nature.com/articles/s41... #SpatialTranscriptomics #CancerResearch cc: @owkin.bsky.social @10xgenomics.bsky.social

nature.com

Transcriptome analysis of archived tumors by Visium, GeoMx DSP, and Chromium reveals patient heterogeneity - Nature Communications

Currently, there is an urgent need to evaluate the strengths and limitations of various probe-based full transcriptome methods for formalin-fixed paraffin-embedded tumor tissues. Here, the authors ana...

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Reposted by Estella Yixing Dong

scverse @scverse.bsky.social · 20/01/2025

@helucro.bsky.social @estellayixingdong.bsky.social @kevinyamauchi.bsky.social @arturmansl.bsky.social Dario Righelli, Louise Deconick, Vincent Carey Should you use R (Bioconductor) or Python (scverse) for spatial omics? Ideally, you won’t have to choose one. We are working toward making...

A presenter showing a slide with a list of R packages for representing spatial omics data, highlighting the problem of fragmentation.

example visualization with ggplot2 of Visium HD data (mouse small intestine) and Merfish prototype pipeline (mouse brain).

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