# CatsCradle <img src="vignettes/CatsCradleLogo.png" alt="" width="200"/> CatsCradle is an R package which provides tools for exploring duality present in single cell datasets. It interfaces with analyses performed with the Seurat Package, although many functions take simple lists, dataframes or matrices as input. In a typical scRNAseq dataset duality exists between cells and the genes they express. Cells are typically assigned cell types based on gene expression; however, programmes of gene expression can cut across cell types. Furthermore, information on how genes are coexpressed can be leveraged to infer functionality. Please see vignette [CatsCradle](vignettes/CatsCradle.Rmd) to find out how you can apply CatsCradle to explore this duality. Even more relationships exist in high resolution spatial transcriptomics datasets, between genes, cells and their position in space. Here we use graph-based representations of cell position, and provide functionality for extending these graphs to account for longer-range interactions. We also provide functions for identifying and exploring neighbourhoods; in terms of gene expression and cell type composition. Finally, we provide tools for analysing ligand-receptor interactions, taking spatial information into account. Please see vignette [CatsCradleSpatial](vignettes/CatsCradleSpatial.Rmd) for details on how to use CatsCradle to analyse spatial data. To dive straight into CatsCradle please see our quickstart vignette [CatsCradleQuickStart](vignettes/CatsCradleQuickStart.Rmd)! ## Installation ``` # Install devtools if (!requireNamespace("devtools", quietly = TRUE)) { install.packages("devtools") } devtools::install_github("AnnaLaddach/CatsCradle") ``` #### Developed by Anna Laddach and Michael Shapiro in the Pachnis lab at the Francis Crick Institute.