Samuel Gunz
@samuelgunz.bsky.social
PhD student in Statistical Bioinformatics at the University of Zurich and the Swiss Institue of Bioinformatics
Reposted by Samuel Gunz
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!
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
November 21, 2025 at 5:31 PM
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!
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Reposted by Samuel Gunz
Orchestrating Spatial Transcriptomics Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.11.20.688607v1
November 21, 2025 at 2:46 PM
Orchestrating Spatial Transcriptomics Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.11.20.688607v1
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...
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
October 14, 2025 at 3:11 PM
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...
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...
Reposted by Samuel Gunz
🚀 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...
📖 Read our pre-print on human tonsil architecture (full of tonsiLove ♥️) here: doi.org/10.1101/2025...
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...
doi.org
September 15, 2025 at 2:40 PM
🚀 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...
📖 Read our pre-print on human tonsil architecture (full of tonsiLove ♥️) here: doi.org/10.1101/2025...
Reposted by Samuel Gunz
We are excited to share the publication of our paper on exploratory spatial statistics for spatial omics data
academic.oup.com/nar/article/...
academic.oup.com/nar/article/...
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
academic.oup.com
September 11, 2025 at 7:04 AM
We are excited to share the publication of our paper on exploratory spatial statistics for spatial omics data
academic.oup.com/nar/article/...
academic.oup.com/nar/article/...
Reposted by Samuel Gunz
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
We discuss the broad range of exploratory spatial statistics options for spatial Omics technologies and show relevant use cases.
arxiv.org/abs/2412.01561
Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta
Spatial omics assays allow for the molecular characterisation of cells in their spatial context. Notably, the two main technological streams, imaging-based and high-throughput sequencing-based, can gi...
arxiv.org
June 27, 2025 at 1:28 PM
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
We discuss the broad range of exploratory spatial statistics options for spatial Omics technologies and show relevant use cases.
arxiv.org/abs/2412.01561
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
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
pasta: Pattern Analysis for Spatial Omics Data
Spatial omics assays allow for the molecular characterisation of cells in their spatial context. Notably, the two main technological streams, imaging-based and high-throughput sequencing-based, can gi...
arxiv.org
December 4, 2024 at 12:14 PM
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
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