Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)

SGS, is a user-friendly, collaborative and versatile browser for visualizing single-cell and spatial multiomics data.

A Toolbox for Spatial Transcriptomics Analysis

BANKSY: spatial clustering

Interactive visualization of spatial omics data

ClusterMap for multi-scale clustering analysis of spatial gene expression

End-to-end analysis of spatial multi-omics data

Spatial analysis toolkit for single cell multiplexed tissue data

Dependency-aware deep generative models for multitasking analysis of spatial genomics data

conST: an interpretable multi-modal contrastive learning framework for spatial transcriptomics

Cell-type Relationship Analysis Workflow Done Across Distances

Spatial Experiments raster - a rasterization preprocessing framework for scalable spatial omics data analysis

Interoperability between SpatialData and the Xenium Explorer

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

a computational framework to identify and characterize cell niches from spatial omics data at single-cell resolution