CatsCradle

CatsCradle exploits the duality between cells and the genes they express to enable spatial transcriptomic analysis and gene clustering in single-cell data.

Key Features:

• Tissue neighbourhood identification: Identifies contiguous regions of tissue surrounding individual cells in spatial transcriptomic data.
• Neighbourhood categorisation: Categorises neighbourhoods by the cell types contained in them and the genes expressed in them.
• Neighbourhood-level Seurat objects: Produces Seurat objects whose individual elements are neighbourhoods rather than cells.
• Gene-level Seurat objects: Produces Seurat objects whose elements are genes to enable categorisation and annotation of genes.
• Gene clustering: Provides tools to cluster genes and visualize relationships between them.
• Gene-cell programme exploration: Explores relationships between gene clusters (programmes) and cell clusters (cell types).
• Data structure compatibility: Interfaces directly with Seurat and SingleCellExperiment data structures.

Scientific Applications:

• Spatial transcriptomics analysis: In-depth analysis of spatial transcriptomic data through neighbourhood-based approaches.
• Gene annotation: Categorisation and annotation of genes through gene-level clustering and visualization.
• Gene programme-cell type relationship analysis: Exploration of relationships between gene clusters (programmes) and cell clusters (cell types).

Methodology:

The package identifies contiguous tissue neighbourhoods surrounding individual cells and produces Seurat objects with neighbourhoods or genes as elements.