MARMOT: A multifaceted R pipeline for analysing spectral flow cytometry data from subcutaneously growing murine gastric organoids

The analysis of murine immune cell types is a critical component of immunological research, necessitating precise and reproducible methodologies. Here, we present a comprehensive protocol and pipeline designed to streamline the process from murine gastric organoid transplant sample preparation to figure generation. This pipeline includes a detailed staining panel tailored for murine immune cells, ensuring accurate and comprehensive identification of various cell types. Additionally, it integrates an R-based analysis script (MARMOT Pipeline), encompassing data processing and visualisation. A key feature of this pipeline is its ability to produce publication-quality figures with minimal direct R coding, thus making advanced data analysis accessible to researchers with limited programming experience. Additionally, figures can be customised using a provided Shiny application. This approach both enhances the efficiency of data analysis and enables the reproducibility required for high-quality scientific research.