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>.
Package details |
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Author | Massimo Andreatta [aut, cre] (<https://orcid.org/0000-0002-8036-2647>), Ariel Berenstein [aut] (<https://orcid.org/0000-0001-8540-5389>), Josep Garnica [aut], Santiago Carmona [aut] (<https://orcid.org/0000-0002-2495-0671>) |
Maintainer | Massimo Andreatta <massimo.andreatta@unil.ch> |
License | GPL-3 |
Version | 1.6.2 |
URL | https://github.com/carmonalab/scGate |
Package repository | View on CRAN |
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