Harmony-R

Harmony-R is a software tool for integrating and analyzing single-cell RNA-seq datasets from diverse sources, technologies, and biological conditions. Key features and benefits of Harmony-R include:

1. Projecting cells into a shared embedding where cells group by cell type rather than dataset-specific conditions, enabling integrated analysis.

2. Simultaneously accounting for multiple experimental and biological factors that may confound analysis when comparing across datasets.

3. Demonstrated superior performance compared to previous data integration algorithms in six analyses.

4. Computationally efficient, integrating around 106 cells across ten datasets on a personal computer.

5. It has been successfully applied to integrate datasets with large experimental differences, studies of specific cell types like pancreatic islet cells, developmental trajectories like mouse embryogenesis, and integration of scRNA-seq with spatial transcriptomics data.