Marker-Based Cell Type Purification for Single-Cell Sequencing Data R package scGate version 1.7.2 A common bioinformatics task in single-cell data analysis is to purify a cell type or cell population of interest from heterogeneous datasets. 'scGate' automatizes marker-based purification of specific cell populations, without requiring training data or reference gene expression profiles. Briefly, 'scGate' takes as input: i) a gene expression matrix stored in a 'Seurat' object and ii) a “gating model” (GM), consisting of a set of marker genes that define the cell population of interest. The GM can be as simple as a single marker gene, or a combination of positive and negative markers. More complex GMs can be constructed in a hierarchical fashion, akin to gating strategies employed in flow cytometry. 'scGate' evaluates the strength of signature marker expression in each cell using the rank-based method 'UCell', and then performs k-nearest neighbor (kNN) smoothing by calculating the mean 'UCell' score across neighboring cells. kNN-smoothing aims at compensating for the large degree of sparsity in scRNA-seq data. Finally, a universal threshold over kNN-smoothed signature scores is applied in binary decision trees generated from the user-provided gating model, to annotate cells as either “pure” or “impure”, with respect to the cell population of interest. See the related publication Andreatta et al. (2022) <doi:10.1093/bioinformatics/btac141>. Software Depends: R (>= 4.3.0) Imports: Seurat (>= 4.0.0), UCell (>= 2.6.0), dplyr, stats, utils, methods, patchwork, ggridges, colorspace, reshape2, ggplot2, BiocParallel Suggests: ggparty, partykit, knitr, rmarkdown Massimo Andreatta <massimo.andreatta@unige.ch> Comprehensive R Archive Network (CRAN) Massimo Andreatta [aut, cre] (ORCID: <https://orcid.org/0000-0002-8036-2647>), Ariel Berenstein [aut] (ORCID: <https://orcid.org/0000-0001-8540-5389>), Josep Garnica [aut], Santiago Carmona [aut] (ORCID: <https://orcid.org/0000-0002-2495-0671>) GPL-3 2025-07-23 application/tgz https://CRAN.R-project.org/package=scGate doi:10.32614/CRAN.package.scGate