Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)
A Toolbox for Spatial Transcriptomics Analysis
SGS, is a user-friendly, collaborative and versatile browser for visualizing single-cell and spatial multiomics data.
BANKSY: spatial clustering
Interactive visualization of spatial omics data
a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challenge of accurately segmenting individual cells in complex imaging datasets, leveraging a unique approach based on graph neural networks (GNNs).
ClusterMap for multi-scale clustering analysis of spatial gene expression
End-to-end analysis of spatial multi-omics data
Dependency-aware deep generative models for multitasking analysis of spatial genomics data
Spatial analysis toolkit for single cell multiplexed tissue data
Cell-type Relationship Analysis Workflow Done Across Distances
conST: an interpretable multi-modal contrastive learning framework for spatial transcriptomics
Interoperability between SpatialData and the Xenium Explorer
Spatial Experiments raster - a rasterization preprocessing framework for scalable spatial omics data analysis
DECIPHER for learning high-fidelity disentangled embeddings from spatial omics data
Patho-DBiT is a platform to spatially decode RNA Biology in archival FFPE tissues.
A Lightweight & Versatile Visualization Tool for Spatial-Omics Data
ClusterMap for multi-scale clustering analysis of spatial gene expression
R package to visualize colocalization for single cell & spatially-resolved genomics data
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