Benchmarking spatial clustering methods with spatially resolved transcriptomics data
Spatial clustering, which shares an analogy with single-cell clustering, has expanded the
scope of tissue physiology studies from cell-centroid to structure-centroid with spatially …
scope of tissue physiology studies from cell-centroid to structure-centroid with spatially …
Clustering spatial transcriptomics data
Motivation Recent advancements in fluorescence in situ hybridization (FISH) techniques
enable them to concurrently obtain information on the location and gene expression of …
enable them to concurrently obtain information on the location and gene expression of …
Benchmarking cell-type clustering methods for spatially resolved transcriptomics data
Spatially resolved transcriptomics technologies enable the measurement of transcriptome
information while retaining the spatial context at the regional, cellular or sub-cellular level …
information while retaining the spatial context at the regional, cellular or sub-cellular level …
Advances in spatial transcriptomic data analysis
Spatial transcriptomics is a rapidly growing field that promises to comprehensively
characterize tissue organization and architecture at the single-cell or subcellular resolution …
characterize tissue organization and architecture at the single-cell or subcellular resolution …
STRIDE: accurately decomposing and integrating spatial transcriptomics using single-cell RNA sequencing
The recent advances in spatial transcriptomics have brought unprecedented opportunities to
understand the cellular heterogeneity in the spatial context. However, the current limitations …
understand the cellular heterogeneity in the spatial context. However, the current limitations …
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 …
Spatially resolved transcriptomes—next generation tools for tissue exploration
M Asp, J Bergenstråhle, J Lundeberg - Bioessays, 2020 - Wiley Online Library
Recent advances in spatially resolved transcriptomics have greatly expanded the
knowledge of complex multicellular biological systems. The field has quickly expanded in …
knowledge of complex multicellular biological systems. The field has quickly expanded in …
Giotto, a pipeline for integrative analysis and visualization of single-cell spatial transcriptomic data
The rapid development of novel spatial transcriptomics technologies has provided new
opportunities to investigate the interactions between cells and their native …
opportunities to investigate the interactions between cells and their native …
SINFONIA: scalable identification of spatially variable genes for deciphering spatial domains
Recent advances in spatial transcriptomics have revolutionized the understanding of tissue
organization. The identification of spatially variable genes (SVGs) is an essential step for …
organization. The identification of spatially variable genes (SVGs) is an essential step for …
Robust decomposition of cell type mixtures in spatial transcriptomics
A limitation of spatial transcriptomics technologies is that individual measurements may
contain contributions from multiple cells, hindering the discovery of cell-type-specific spatial …
contain contributions from multiple cells, hindering the discovery of cell-type-specific spatial …