NiCo

NiCo integrates single-cell resolution spatial transcriptomics with matched single-cell RNA-sequencing data to infer the influence of the spatial niche on the cell state.

Key Features:

• Niche covariation analysis: Identifies extrinsic drivers of cell state modulation by analyzing crosstalk between individual cell types within the same niche.
• Spatial transcriptomics integration: Combines single-cell resolution spatial transcriptomics with matched single-cell RNA-sequencing reference data.
• Cell state prediction: Predicts novel niche interactions that govern cell state variation underlying tissue development and homeostasis.

Scientific Applications:

• Developmental biology: Elucidates tissue architecture and cell fate regulation during mouse embryogenesis.
• Tissue homeostasis: Identifies drivers of cellular states in local niches in adult small intestine and liver.
• Cell-cell interaction discovery: Predicts feedback mechanisms between cell types, such as the Kupffer cell-stellate cell interaction that dampens stellate cell activation in normal liver.

Methodology:

NiCo performs niche covariation analysis to integrate single-cell resolution spatial transcriptomics with matched single-cell RNA-sequencing reference data.