scGate

scGate is an R package that automates the purification of specific cell populations from heterogeneous single-cell datasets. It uses a hierarchical set of markers, similar to gating strategies in flow cytometry, to isolate cell types or populations of interest without requiring training data or reference gene expression profiles. scGate can be applied to various single-cell data modalities, such as RNA-seq, ATAC-seq, and CITE-seq, and outperforms state-of-the-art single-cell classifiers. The package is integrated with the Seurat framework, providing a user-friendly tool for researchers to isolate desired cell populations from complex single-cell datasets.