SeuratIntegrate: an R package to facilitate the use of integration methods with Seurat

Abstract Motivation Integrating multiple datasets has become an increasingly common task in scRNA-seq analysis. The advent of single-cell atlases adds further complexity, as they often involve combining data with nested batch effects. While common tools such as Seurat offer access to batch-correction methods, the diversity of available options remains limited. With growing evidence that integration method performance varies significantly between datasets, making an informed decision in selecting the most appropriate integration approach is not trivial. A broader range of accessible methods combined with a comprehensive toolbox for comparative integration analysis, would support more effective and flexible single-cell data integration workflows. Results Built on Seurat’s foundations, we developed SeuratIntegrate, an open source R package that expands integration methods available to Seurat users, including Python-based approaches, while operating entirely within the R environment. The package enables integration benchmarking using well-established performance metrics, and provides automated Python environment management, cross-language object conversion, and tools for score handling and visualization. All features are designed for ease of use and extensibility. Availability and implementation The source code, installation process and vignettes demonstrating usage are freely available on GitHub: https://github.com/cbib/Seurat-Integrate. A Zenodo deposit contains a copy of the package code along with the data to reproduce the results presented above (accession 10.5281/zenodo.14288360). The package is released under the MIT License.