spatial

Integrating gene expression and imaging data across Visium capture areas with visiumStitched
Background Visium is a widely-used spatially-resolved transcriptomics assay available from 10x Genomics. Standard Visium capture areas …
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Integrating gene expression and imaging data across Visium capture areas with visiumStitched
Lessons from spatially-resolved transcriptomics of postmortem human brain data projects
Last updated on Mon, Aug 12, 2024
Project Slides
Lessons from spatially-resolved transcriptomics of postmortem human brain data projects
A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex
The molecular organization of the human neocortex historically has been studied in the context of its histological layers. However, …
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A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex
HumanPilot: first spatially-resolved transcriptomics study using Visium
Would you prefer a video walkthrough over reading this blog post? Check out this explainer video 🎥 A few years ago now (2021) we published a study we refer to with a very generic name: HumanPilot (Maynard, Collado-Torres, Weber, Uytingco et al.
Last updated on Sat, May 25, 2024 13 min read Science, LIBD
Project
2024 Current Topics in Biostatistics guest seminar
Thanks @kenzhou86 & Margaret Taub for inviting to present at the Current Topics in Biostatistics seminar It was fun reminiscing about the past & sharing my experience. Got them to laugh a few times ^^
Last updated on Mon, Feb 26, 2024
Project Slides
2024 Current Topics in Biostatistics guest seminar
The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics
Norepinephrine (NE) neurons in the locus coeruleus (LC) make long-range projections throughout the central nervous system, playing …
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The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics
escheR: Unified multi-dimensional visualizations with Gestalt principles
The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are …
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escheR: Unified multi-dimensional visualizations with Gestalt principles
Spatiotemporal analysis of gene expression in the human dentate gyrus reveals age-associated changes in cellular maturation and neuroinflammation
The dentate gyrus of the hippocampus is important for many cognitive functions, including learning, memory, and mood. Here, we …
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Spatiotemporal analysis of gene expression in the human dentate gyrus reveals age-associated changes in cellular maturation and neuroinflammation
VistoSeg: Processing utilities for high-resolution images for spatially resolved transcriptomics data
Spatially resolved transcriptomics (SRT) is a growing field that links gene expression to anatomical context. SRT approaches that use …
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VistoSeg: Processing utilities for high-resolution images for spatially resolved transcriptomics data
Influence of Alzheimer's Disease Related Neuropathology on Local Microenvironment Gene Expression in the Human Inferior Temporal Cortex
Neuropathological lesions in the brains of individuals affected with neurodegenerative disorders are hypothesized to trigger molecular …
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Influence of Alzheimer's Disease Related Neuropathology on Local Microenvironment Gene Expression in the Human Inferior Temporal Cortex