scGate: Marker-Based Cell Type Purification for Single-Cell Sequencing Data (original) (raw)
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>.
| Version: | 1.6.2 |
|---|---|
| Depends: | R (≥ 4.3.0) |
| Imports: | Seurat (≥ 4.0.0), UCell (≥ 2.6.0), dplyr, stats, utils, methods, patchwork, ggridges, reshape2, ggplot2, BiocParallel |
| Suggests: | ggparty, partykit, knitr, rmarkdown |
| Published: | 2024-04-23 |
| DOI: | 10.32614/CRAN.package.scGate |
| Author: | Massimo Andreatta  [aut, cre], Ariel Berenstein [aut], Josep Garnica [aut], Santiago Carmona [aut] |
| Maintainer: | Massimo Andreatta <massimo.andreatta at unil.ch> |
| BugReports: | https://github.com/carmonalab/scGate/issues |
| License: | GPL-3 |
| URL: | https://github.com/carmonalab/scGate |
| NeedsCompilation: | no |
| Citation: | scGate citation info |
| Materials: | NEWS |
| CRAN checks: | scGate results |
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