SpatialPrompt – spatially aware scalable and accurate tool for spot deconvolution and domain identification in spatial transcriptomics
In the world of biology, understanding the details of how cells function and interact within…
Browsing: Spatial Analysis
SPADE – spatial deconvolution for domain specific cell-type estimation
In genomics, understanding how genes are expressed in different cell types within their spatial context…
New method tags cells with location coordinates for single-cell studies
The technique, called Slide-tags, allows scientists to map the location of cells within tissues in…
standR – spatial transcriptomic analysis for GeoMx DSP data
To gain a better understanding of the complexity of gene expression in normal and diseased…
CeLEry – leveraging spatial transcriptomics data to recover cell locations in single-cell RNA-seq
Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular heterogeneity in health and disease.…
spSeudoMap – cell type mapping of spatial transcriptomics using unmatched single-cell RNA-seq data
Since many single-cell RNA-seq (scRNA-seq) data are obtained after cell sorting, such as when investigating…
SiT – spatial isoform transcriptomics
In situ capturing technologies add tissue context to gene expression data, with the potential of…
AllenDigger – spatial expression data visualization, spatial heterogeneity delineation, and single-cell registration based on the Allen Brain Atlas
Spatial transcriptomics can be used to capture cellular spatial organization and has facilitated new insights…
SRTsim – spatial pattern preserving simulations for spatially resolved transcriptomics
Spatially resolved transcriptomics (SRT)-specific computational methods are often developed, tested, validated, and evaluated in silico…
GraphST – spatially informed clustering, integration, and deconvolution of spatial transcriptomics
Spatial transcriptomics technologies generate gene expression profiles with spatial context, requiring spatially informed analysis tools…