# Battlefield <img width="160" height="160" src="man/figures/logo.png" align="right" /> <br/> <br/> ## Overview **Battlefield** is a Swiss-army toolkit designed to define and extract spatial spots from specific regions in spatial transcriptomics data. </br></br> It provides low-level, modular utilities to delineate spatial regions of interest, including **interfaces between clusters**, **intra-cluster layers**, and **inter-cluster trajectories**. </br></br> These utilities are intended to be reused and composed within higher-level analytical workflows and packages. </br></br> `Battlefield` supports sequencing-based spatial transcriptomics platforms such as **10x Genomics Visium**, across multiple resolutions, including Visium HD (binned). <img src="man/figures/workflow.png" align="center" width="100%" height="100%" /> **Battlefield** provides four core functionalities to define and extract spatial transcriptomics spots from specific tissue regions, enabling the study of spatial organization under different biological contexts: * **Interfaces between clusters** — identify and analyze boundary regions where distinct tissue or cell populations interact. * **Intra-cluster layers** — characterize spatial layers or gradients within a single cluster. * **Inter-cluster trajectories** — model spatial transitions across multiple clusters. * **Cluster neighbourhood** — report the cluster composition of a spatial neighborhood defined by k nearest spots, constrained by a distance threshold. It can be integrated upstream to support insightful ligand–receptor analyses, using BulkSignalR, available from Bioconductor [here](https://www.bioconductor.org/packages/release/bioc/html/BulkSignalR.html). Data summary functions are proposed to help defining spatial regions of interest on the top of previously defined clusters. ## Installation ``` R # Battlefield directly from Bioconductor. if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("Battlefield") # or development version via GitHub: # install.packages("devtools") devtools::install_github("ZheFrench/Battlefield",build_vignettes = TRUE) # To read the vignette # browseVignettes("Battlefield") ``` ## Changes Major changes are reported in the [NEWS file](https://github.com/ZheFrench/Battlefield/blob/master/NEWS), make sure to check it out if you want to follow the latest developments. ## Issues and bug reports Please use https://github.com/ZheFrench/Battlefield/issues to submit issues, bug reports, and comments. **Battlefield** has been successfully installed on Mac OS X, Linux, and Windows using R version 4.5. The code in this repository is published with the [CeCILL](https://github.com/ZheFrench/Battlefield/blob/master/LICENSE.md) License. <!-- badges: start --> [](https://shields.io/) <!-- badges: end -->