# Capturing gene–cell duality in a cat’s cradle

## TL;DR

CatsCradle is an R package for analyzing single-cell data by exploring the relationship between genes and cell types.

## Contribution

It introduces a new approach to gene clustering and visualization in single-cell analysis.

## Key findings

- The package allows clustering genes and visualizing their relationships.
- It connects gene clusters with cell clusters to explore biological programmes.
- CatsCradle integrates with existing tools like Seurat and SingleCellExperiment.

## Abstract

CatsCradle is an R package for single-cell analysis that exploits the duality between cells and the genes they express. Our package provides tools to cluster genes, visualize relationships between them, and to explore relationships between gene clusters (programmes) and cell clusters (cell types).

CatsCradle is available freely as an R Bioconductor package (https://bioconductor.org/packages/CatsCradle) and interfaces directly with Seurat (Hao et al. 2024) and SingleCellExperiment (Amezquita et al. 2020) data structures.