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Exploring tissue architecture using spatial transcriptomics
Spatial omics data are clustered to define both cell types and tissue domains. We present
Building Aggregates with a Neighborhood Kernel and Spatial Yardstick (BANKSY), an …
Building Aggregates with a Neighborhood Kernel and Spatial Yardstick (BANKSY), an …
Clinical and translational values of spatial transcriptomics
L Zhang, D Chen, D Song, X Liu, Y Zhang… - … and Targeted Therapy, 2022 - nature.com
The combination of spatial transcriptomics (ST) and single cell RNA sequencing (scRNA-
seq) acts as a pivotal component to bridge the pathological phenomes of human tissues with …
seq) acts as a pivotal component to bridge the pathological phenomes of human tissues with …
SCS: cell segmentation for high-resolution spatial transcriptomics
Spatial transcriptomics promises to greatly improve our understanding of tissue organization
and cell–cell interactions. While most current platforms for spatial transcriptomics only offer …
and cell–cell interactions. While most current platforms for spatial transcriptomics only offer …
Cell clustering for spatial transcriptomics data with graph neural networks
Spatial transcriptomics data can provide high-throughput gene expression profiling and the
spatial structure of tissues simultaneously. Most studies have relied on only the gene …
spatial structure of tissues simultaneously. Most studies have relied on only the gene …
BASS: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies
Spatial transcriptomic studies are reaching single-cell spatial resolution, with data often
collected from multiple tissue sections. Here, we present a computational method, BASS …
collected from multiple tissue sections. Here, we present a computational method, BASS …
Annotation of spatially resolved single-cell data with STELLAR
Accurate cell-type annotation from spatially resolved single cells is crucial to understand
functional spatial biology that is the basis of tissue organization. However, current …
functional spatial biology that is the basis of tissue organization. However, current …
[HTML][HTML] A guidebook of spatial transcriptomic technologies, data resources and analysis approaches
Advances in transcriptomic technologies have deepened our understanding of the cellular
gene expression programs of multicellular organisms and provided a theoretical basis for …
gene expression programs of multicellular organisms and provided a theoretical basis for …
SONAR enables cell type deconvolution with spatially weighted Poisson-Gamma model for spatial transcriptomics
Recent advancements in spatial transcriptomic technologies have enabled the
measurement of whole transcriptome profiles with preserved spatial context. However …
measurement of whole transcriptome profiles with preserved spatial context. However …