Capturing gene–cell duality in a cat’s cradle

Journal article

Summary: 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). Availability and implementation: 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.

Authors: Laddach, A; Progatzky, F; Pachnis, V; Shapiro, M

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Oxford University Press
• Journal: Bioinformatics
• Volume: 42
• Issue: 1
• Pages: btaf681
• Article number: btaf681
• Publication date: 2026-01-11
• Acceptance date: 2025-12-17
• DOI: 10.1093/bioinformatics/btaf681
• EISSN: 1367-4811
• ISSN: 1367-4803
• Language: English
• Keywords: Bioconductor; Duality (order theory); R package; Exploit; Cluster (spacecraft); Software