SPECTRE

Spectre is an R package designed to provide a comprehensive and scalable approach to analyzing high-dimensional cytometry data. It allows for the integration and analysis of data from multiple batches or experiments, including flow cytometry, mass cytometry (CyTOF), spectral cytometry, single-cell RNA sequencing (scRNAseq), and high-dimensional imaging technologies like Imaging Mass Cytometry (IMC). The package includes features for raw data pre-processing, batch alignment, data integration, clustering, dimensionality reduction, visualization, and population labeling, as well as quantitative and statistical analysis. Its modular design makes it accessible to both bioinformaticians and laboratory scientists. Spectre is available as an R package or Docker container, with R code available on GitHub at .